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1.  A Computer Model of Insect Traps in a Landscape 
Scientific Reports  2014;4:7015.
Attractant-based trap networks are important elements of invasive insect detection, pest control, and basic research programs. We present a landscape-level, spatially explicit model of trap networks, focused on detection, that incorporates variable attractiveness of traps and a movement model for insect dispersion. We describe the model and validate its behavior using field trap data on networks targeting two species, Ceratitis capitata and Anoplophora glabripennis. Our model will assist efforts to optimize trap networks by 1) introducing an accessible and realistic mathematical characterization of the operation of a single trap that lends itself easily to parametrization via field experiments and 2) allowing direct quantification and comparison of sensitivity between trap networks. Results from the two case studies indicate that the relationship between number of traps and their spatial distribution and capture probability under the model is qualitatively dependent on the attractiveness of the traps, a result with important practical consequences.
PMCID: PMC4228344  PMID: 25388652
2.  Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets 
BMC Genomics  2014;15(1):942.
The oriental fruit fly, Bactrocera dorsalis, is an important pest of fruit and vegetable crops throughout Asia, and is considered a high risk pest for establishment in the mainland United States. It is a member of the family Tephritidae, which are the most agriculturally important family of flies, and can be considered an out-group to well-studied members of the family Drosophilidae. Despite their importance as pests and their relatedness to Drosophila, little information is present on B. dorsalis transcripts and proteins. The objective of this paper is to comprehensively characterize the transcripts present throughout the life history of B. dorsalis and functionally annotate and analyse these transcripts relative to the presence, expression, and function of orthologous sequences present in Drosophila melanogaster.
We present a detailed transcriptome assembly of B. dorsalis from egg through adult stages containing 20,666 transcripts across 10,799 unigene components. Utilizing data available through Flybase and the modENCODE project, we compared expression patterns of these transcripts to putative orthologs in D. melanogaster in terms of timing, abundance, and function. In addition, temporal expression patterns in B. dorsalis were characterized between stages, to establish the constitutive or stage-specific expression patterns of particular transcripts. A fully annotated transcriptome assembly is made available through NCBI, in addition to corresponding expression data.
Through characterizing the transcriptome of B. dorsalis through its life history and comparing the transcriptome of B. dorsalis to the model organism D. melanogaster, a database has been developed that can be used as the foundation to functional genomic research in Bactrocera flies and help identify orthologous genes between B. dorsalis and D. melanogaster. This data provides the foundation for future functional genomic research that will focus on improving our understanding of the physiology and biology of this species at the molecular level. This knowledge can also be applied towards developing improved methods for control, survey, and eradication of this important pest.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-942) contains supplementary material, which is available to authorized users.
PMCID: PMC4223851  PMID: 25348373
3.  Male motion coordination in anopheline mating swarms 
Scientific Reports  2014;4:6318.
The Anopheles gambiae species complex comprises the primary vectors of malaria in much of sub-Saharan Africa. Most of the mating in these species occurs in swarms composed almost entirely of males. Intermittent, organized patterns in such swarms have been observed, but a detailed description of male-male interactions has not previously been available. We identify frequent, time-varying interactions characterized by periods of parallel flight in data from 8 swarms of Anopheles gambiae and 3 swarms of Anopheles coluzzii filmed in 2010 and 2011 in the village of Donéguébogou, Mali. We use the cross correlation of flight direction to quantify these interactions and to induce interaction graphs, which show that males form synchronized subgroups whose size and membership change rapidly. A swarming model with damped springs between each male and the swarm centroid shows good agreement with the correlation data, provided that local interactions represented by damping of relative velocity between males are included.
PMCID: PMC4161964  PMID: 25212874
4.  An agent-based simulation of extirpation of Ceratitis capitata applied to invasions in California 
Journal of Pest Science  2013;87(1):39-51.
We present an agent-based simulation (ABS) of Ceratitis capitata (“Medfly”) developed for estimating the time to extirpation of this pest in areas where quarantines and eradication treatments were immediately imposed. We use the ABS, implemented in the program MED-FOES, to study seven different outbreaks that occurred in Southern California from 2008 to 2010. Results are compared with the length of intervention and quarantine imposed by the State, based on a linear developmental model (thermal unit accumulation, or “degree-day”). MED-FOES is a useful tool for invasive species managers as it incorporates more information from the known biology of the Medfly, and includes the important feature of being demographically explicit, providing significant improvements over simple degree-day calculations. While there was general agreement between the length of quarantine by degree-day and the time to extirpation indicated by MED-FOES, the ABS suggests that the margin of safety varies among cases and that in two cases the quarantine may have been excessively long. We also examined changes in the number of individuals over time in MED-FOES and conducted a sensitivity analysis for one of the outbreaks to explore the role of various input parameters on simulation outcomes. While our implementation of the ABS in this work is motivated by C. capitata and takes extirpation as a postulate, the simulation is very flexible and can be used to study a variety of questions on the invasion biology of pest insects and methods proposed to manage or eradicate such species.
PMCID: PMC3925300  PMID: 24563646
Simulation; Model; Medfly; Quarantine; Agent-based modeling
5.  A Python module to normalize microarray data by the quantile adjustment method 
Microarray technology is widely used for gene expression research targeting the development of new drug treatments. In the case of a two-color microarray, the process starts with labeling DNA samples with fluorescent markers (cyanine 635 or Cy5 and cyanine 532 or Cy3), then mixing and hybridizing them on a chemically treated glass printed with probes, or fragments of genes. The level of hybridization between a strand of labeled DNA and a probe present on the array is measured by scanning the fluorescence of spots in order to quantify the expression based on the quality and number of pixels for each spot. The intensity data generated from these scans are subject to errors due to differences in fluorescence efficiency between Cy5 and Cy3, as well as variation in human handling and quality of the sample. Consequently, data have to be normalized to correct for variations which are not related to the biological phenomena under investigation. Among many existing normalization procedures, we have implemented the quantile adjustment method using the python computer language, and produced a module which can be run via an HTML dynamic form. This module is composed of different functions for data files reading, intensity and ratio computations and visualization. The current version of the HTML form allows the user to visualize the data before and after normalization. It also gives the option to subtract background noise before normalizing the data. The output results of this module are in agreement with the results of other normalization tools.
PMCID: PMC3087835  PMID: 20970526
module; quantile method; python; microarray; normalization
6.  Seasonal Climate Effects Anemotaxis in Newly Emerged Adult Anopheles gambiae Giles in Mali, West Africa 
PLoS ONE  2011;6(11):e26910.
The direction and magnitude of movement by the malaria vector Anopheles gambiae Giles has been of great interest to medical entomologists for over 70 years. This direction of movement is likely to be affected by many factors, from environmental conditions and stage of life history of the mosquito to the existence of attractants in the vicinity. We report here the direction of movement of newly emerged An. gambiae in nature, around the village of Donéguébougou, Mali. We assessed the direction of movement for individual mosquitoes by placing them in a novel enclosure with exit traps oriented in the direction of the cardinal and intermediate points of the compass. We consistently found predominantly Southward directions of movement during 2009 and 2010, with an additional Eastward component during the dry season and a Westward one during the wet season. Our data indicate that wind has an important effect on the direction of movement, but that this effect varied by season: Average directions of movement were downwind during the dry season and upwind during the wet season. A switch in anemotactic response suggests that the direction of movement of An. gambiae relative to the wind immediately after emergence under varying conditions of humidity should be further investigated under controlled conditions.
PMCID: PMC3217951  PMID: 22114663
7.  A further insight into the sialome of the tropical bont tick, Amblyomma variegatum 
BMC Genomics  2011;12:136.
Ticks--vectors of medical and veterinary importance--are themselves also significant pests. Tick salivary proteins are the result of adaptation to blood feeding and contain inhibitors of blood clotting, platelet aggregation, and angiogenesis, as well as vasodilators and immunomodulators. A previous analysis of the sialotranscriptome (from the Greek sialo, saliva) of Amblyomma variegatum is revisited in light of recent advances in tick sialomes and provides a database to perform a proteomic study.
The clusterized data set has been expertly curated in light of recent reviews on tick salivary proteins, identifying many new families of tick-exclusive proteins. A proteome study using salivary gland homogenates identified 19 putative secreted proteins within a total of 211 matches.
The annotated sialome of A. variegatum allows its comparison to other tick sialomes, helping to consolidate an emerging pattern in the salivary composition of metastriate ticks; novel protein families were also identified. Because most of these proteins have no known function, the task of functional analysis of these proteins and the discovery of novel pharmacologically active compounds becomes possible.
PMCID: PMC3060141  PMID: 21362191
8.  Population Size and Migration of Anopheles gambiae in the Bancoumana Region of Mali and Their Significance for Efficient Vector Control 
PLoS ONE  2010;5(4):e10270.
We present results of two intensive mark-release-recapture surveys conducted during the wet and dry seasons of 2008 in the villages of Fourda and Kenieroba, Mali. The former is a small fishing village by the Niger River with a moderate to high densities of Anopheles gambiae Giles s.s. (Diptera: Culicidae) throughout the year, while the latter is a large agricultural community 2 km inland that experiences strong seasonal fluctuation in An. gambiae densities. We estimate the population size of female An. gambiae in Fourda to be in less than 3,000 during the dry season. We found evidence of large population size and migration from Fourda in Kenieroba during the wet season, but very low numbers and no sign of migrants during the dry season. We suggest that malaria vector control measures aimed at adult mosquitoes might be made more efficient in this region and other seasonal riparian habitats by targeting disruption of mosquito populations by the river during the dry season. This would decrease the size of an already small population, and would be likely to delay the explosive growth in vector numbers in the larger inland villages as rainfall increases.
PMCID: PMC2858161  PMID: 20422013
9.  Structure and Dynamics of Male Swarms of Anopheles gambiae 
Journal of medical entomology  2009;46(2):227-235.
Mosquito swarms are poorly understood mating aggregations. In the malaria vector Anopheles gambiae Giles, they are known to depend on environmental conditions, such as the presence of a marker on the ground, and they may be highly relevant to reproductive isolation. We present quantitative measurements of individual An. gambiae positions within swarms from Donéguébougou, Mali, estimated by stereoscopic video image analysis. Results indicate that swarms in this species are approximately spherical, with an unexpectedly high density of individuals close to the swarm centroid. This high density may be the result of individual males maximizing their probability of encountering a female or a product of mosquito orientation through cues within the swarm. Our analysis also suggests a difference in swarm organization between putative incipient species of An. gambiae with increasing numbers of males. This may be related to a difference in marker use between these groups, supporting the hypothesis that swarming behavior is a mechanism of mate recognition and ultimately reproductive isolation.
PMCID: PMC2680012  PMID: 19351073
Anopheles gambiae; swarm; mate recognition; three-dimensional localization; stereoscopic image analysis
10.  FORMATOMATIC: a program for converting diploid allelic data between common formats for population genetic analysis 
Molecular ecology notes  2007;7(4):592-593.
There has been a great increase in both the number of population genetic analysis programs and the size of data sets being studied with them. Since the file formats required by the most popular and useful programs are variable, automated reformatting or conversion between them is desirable. formatomatic is an easy to use program that can read allelic data files in genepop, raw (csv) or convert formats and create data files in nine formats: raw (csv), arlequin, genepop, immanc/bayesass +, migrate, newhybrids, msvar, baps and structure. Use of formatomatic should greatly reduce time spent reformatting data sets and avoid unnecessary errors.
PMCID: PMC2753541  PMID: 19789658
allele; conversion; data file; format; genotype; population genetic
11.  Spatial swarm segregation and reproductive isolation between the molecular forms of Anopheles gambiae 
Anopheles gambiae, the major malaria vector in Africa, can be divided into two subgroups based on genetic and ecological criteria. These two subgroups, termed the M and S molecular forms, are believed to be incipient species. Although they display differences in the ecological niches they occupy in the field, they are often sympatric and readily hybridize in the laboratory to produce viable and fertile offspring. Evidence for assortative mating in the field was recently reported, but the underlying mechanisms awaited discovery. We studied swarming behaviour of the molecular forms and investigated the role of swarm segregation in mediating assortative mating. Molecular identification of 1145 males collected from 68 swarms in Donéguébougou, Mali, over 2 years revealed a strict pattern of spatial segregation, resulting in almost exclusively monotypic swarms with respect to molecular form. We found evidence of clustering of swarms composed of individuals of a single molecular form within the village. Tethered M and S females were introduced into natural swarms of the M form to verify the existence of possible mate recognition operating within-swarm. Both M and S females were inseminated regardless of their form under these conditions, suggesting no within-mate recognition. We argue that our results provide evidence that swarm spatial segregation strongly contributes to reproductive isolation between the molecular forms in Mali. However this does not exclude the possibility of additional mate recognition operating across the range distribution of the forms. We discuss the importance of spatial segregation in the context of possible geographic variation in mechanisms of reproductive isolation.
PMCID: PMC2821344  PMID: 19734189
molecular forms; Anopheles gambiae; reproductive isolation; swarms
12.  Is Vector Body Size the Key to Reduced Malaria Transmission in the Irrigated Region of Niono, Mali? 
Journal of medical entomology  2006;43(5):820-827.
Malaria vectors can reach very high densities in villages near irrigated rice fields in Africa, leading to the expectation that malaria should be especially prevalent there. Surprisingly, this is not always the case. In Niono, Mali, villages from nonirrigated areas have higher malaria prevalence than those within the irrigated regions, which suffer from higher mosquito numbers. One hypothesis explaining this observation is that mosquitoes from irrigated fields with high densities are inefficient vectors. This could occur if higher larval densities lead to smaller mosquitoes that suffer elevated mortality. Three predictions of the hypothesis were studied. First, the effect of larval density on larval body size was measured for both Anopheles gambiae Giles and Anopheles funestus Giles. Second, the relationship between larval and adult body size was tested. Third, evidence of an effect of adult size on survivorship in both irrigated and nonirrigated villages during the wet and dry seasons was sought. There was a modest positive relationship between densities of immatures and larval size, and a strong relationship between larval and adult size. Furthermore, adult survivorship was higher in nonirrigated areas. However, there was no effect of size on survivorship between comparable samples from both the irrigated and nonirrigated zones. Although density may have a causal relationship with reduced transmission in the irrigated areas of Niono, it is unlikely to be because higher density leads to smaller body size and lower survivorship.
PMCID: PMC2730943  PMID: 17017214
Anopheles; irrigation; size; density; survivorship

Results 1-12 (12)