Research

Blow Fly Genomics

Without understanding the basic genetic makeup of the fly, we are at odds to understand how it performs in any given environment, why it evolved and adapted, and how we can use the fly to make inferences of predictions about its development resource (carrion). As such, it is my reserach laboratory's goals to generate genetic reference datasets (= genomes) to begin to understand the structure-function relationships in blow flies with respect to certain life history traits. Below is a tale of four species:

 

Phormia regina

Phormia regina (Diptera: Calliphoridae) is one of the most common carrion blow flies and forensic indicator species for most of the United States and Canada due to its distribution and abundance. Because of this, it is often used to estimate the minimum postmortem interval (minPMI) based on its develpmental timing. This is done through the use of reference development data sets (of which there are many). The issue is that there is a lot of variation that exists within individual developmental stages that result in less precise estimates of age, the developmental phenotype most often used by forensic entomologists.

Assembly Statistics Female Male
Number of contigs
192,662
187,700
N50
7,918 bp
7,177 bp
Mapped Reads (%)
98%
97%
CEGMA (complete, %)
94%
97%
Coverage
44X
44X

 

GOALS: Generate a high quality genome to isolate and characterize more robust markers of population genetic structure to understand perturbations on development rate; and

Isolate and characterize a genetic sex marker for use to improve precision in age determinations using immature development data.

Cochliomyia macellaria

Cochliomyia macellaria (Diptera: Calliphoridae) is another common carrion blow fly, but is also known as the secondary screwworm fly for its close evolutioonary history to the primary screwworm fly, Cochliomyia hominivorax. This fly is also commonly encountered at decomposed remains, and thus serves as a forensic indicator species for minPMI. Our investigation into this species is the determination of the genetic effect on development time variation. We did by purposely introducing variation through selection for fast and slow development, then through de novo genome assembly/resequencing efforts, isolate significantly diverged loci for a better understanding of how development varies. This is a collaborative project with Texas A&M University's Aaron Tarone funded through the National Institute of Justice (2012-DN-BX-K024).

With these now sequence libraries (9 in total), we can take a candidate gene approach to look at the structure of known deelopmental genes, find genetic markers, and test our hypotheses of the correlation between structure and function in validation selection lines.

 

Chrysomya rufifacies

Chrysomya rufifacies (Diptera: Calliphoridae), our third species, has an interesting life history trait that is likely an important outbreeding strategy, thus potentially maintaining a greater amount of genetic vairation in the population. This fly is monogenic, which means that the female produce only 1 sex of offspring: either only female or only male offspring. The sex determination pathway that leads to this trait remains elusive. Thus, our goals were to generate de novo genome assemblies of both types of females, as well as males, to understand the structure of the genome and how it produces this trait. While we work on generating and assembling genomes, our collaborators ( Drs A Tarone, Texas A&M University and M Pimsler ,University of Alabama) work on expression analyses from their RNAseq experiments. So far, we have seen some major differences in structure of historically important sex determination genes - and are in the proces of validating our genome data.

 

Lucilia cuprina

Lucilia cuprina (Diptera: Calliphoridae) is likely the most interesting blow fly on this list. It is a well known pest of sheep in some parts of the world, it has drastically dimorphic sex chromosomes (to the tune of 100Mbp difference between male and female flies, Picard et al, 2012), and it hybridizes, in the wild, with another closely related, forensically important fly, Lucilia sericata. Furthermore, with its worldwide distribution and its ability to colonize carrion immediately, is a forensic indicator species. Yet, we do not know much about its evolutionary history. The goals of this work are to generate a high quality genome of the North American L. cuprina fly, one in which we know ancestrally was a carrion breeder, to better understand the adaptations necessary to make the jump to the ectoparasitic lifestyle.

 

Number Contigs
88,495
N50
24,771 bp
Average Coverage
30X

 

 

Species and Age Determination of Blow Fly Pupae

The study of insects found on a body can yield valuable information about the time and circumstances of death. In forensic entomological investigations, the oldest of such insects are traditionally collected from the corpse, their species and age determined, and a postmortem interval (PMI) can be estimated. In most cases, these insects are flies of the Dipteran family Calliphoridae. The determination of the PMI is based on the assumption that the oldest specimen from the body is collected, and this is often pupae.  Pupae are notoriously difficult to use as casework samples, as it is generally difficult to identify their species, and determining the age of a pupa either requires expertise not generally available.   This work proposes a simple, fast, and cost-effective technique for identifying the species and age of fly pupae via the analysis of volatile organic compounds (VOCs).  These compounds are given off by the cuticle—the protective “skin” of the insect.  Previous research has shown these compounds are capable of identifying flies with a high degree of discrimination (Moore, Adam et al. 2013). But, because little is known about variations in VOC profiles over time and under a varying set of conditions, this work seeks to investigate the effects of several biotic and abiotic variables on the suite of VOCs synthesized and emitted by flies. The influence of diet, pupation substrate, temperature, light, and humidity will be independently evaluated, and the VOCs observed for each variable will be subject to rigorous statistical treatment via chemometric methods. This will allow for the isolation of a subset of VOCs that are relatively unaffected by changes in environment, which can be used for identification in entomological investigations regardless of region or climate.

VOC

 

Hermetia illucens

Hermetia illucens (Diptera: Stratiomyidae), also known as the black soldier fly, is also common and widespread (with worldwide distributions). Though it does make the occassional appearance at carrion, it is more likely to be found in compost heaps. Thier most important contributions are to efficiently bioconvert organic waste material into protein. Many labs around the world are working to incorporate BSF as an alternative mean to produce protein for livestock, poultry and aquaculture purposes. Our lab is dedicated to studying their population structure in the hopes of identifying correlations between optimal phenotypes (such as the ability to develop quickly and efficiently in "culture") and genotypes identified via novel microsatellites isolated and characterized in our lab.

 

Publications

 

AA Andere, RN Platt II, DA Ray, CJ Picard (2016) "Genome sequence of Phormia regina (Diptera: Calliphoridae): Implications for medical, veterinary and forensic research." BMC Genomics, 17: 842. http://rdcu.be/l59V

CG Owings, CJ Picard (2016) "Temporal survey of a carrion beetle (Coleoptera: Silphidae) community in Indiana. Proceedings of the Indiana Academy of Science. 124(2).

JK Tomberlin, A van Huis, ME Benbow, H Jordan, DA Astuti, D Azzollini, I Banks, V Bava, C Borgemeister, JA Cammack, RS Chapkin, H Cickova, TL Crippen, A Day, M Dicke, DJW Drew, C Emhart, M Epstein, M Finke, CH Fischer, D Gatlin, NTh Grabowski, C He, L Heckman, A Hubert, J Jacobs, J Josephs, SK Khanal, J-F Kleinfinger, G Klein, C Leach, Y Liu, GL Newton, R Olivier, JL Pechal, CJ Picard, S Rojo, A Roncarati, C Sheppard, AM Tarone, B Verstappen, A Vickerson, H Yang, AL Yen, Z Yu, J Zhang, L Zheng. (2015) "Protecting the environment through insect farming as a means to produce protein for use as livestock, poultry, and aquaculture feed". Journal of Insects as Food and Feed, 1(4): 307-309.

AM Salam, FK Adham, CJ Picard (2015) “Survey of the genetic diversity of forensically important Chrysomya blow flies from Egypt.”  Journal of Medical Entomology, 1-9, DOI: 10.1093/jme/tjv013.

K Faulds, J.D. Wells, CJ Picard (2014) "Verification of AFLP kinship methods of entomological evidence by sequencing." Forensic Science International: Genetics. 245: 58-62.

G.M. Dembinski, CJ Picard (2014) "Evaluation of the IrisPlex DNA-based eye color prediction assay in a United States population." Forensic Science International: Genetics. 9: 111-117.

CJ Picard. (2013) "First record of Chrysomya megacephala Fabricius (Diptera: Calliphoridae) in Indiana, U.S.A." Proceedings of the Entomological Society of Washington, 115(3): 265-267.

CJ Picard, K DeBlois, F Tovar, JS Johnston, AM Tarone. (2013) “Increasing precision in PMI estimates: What’s sex got to do with it?”.   Journal of Medical Entomology, 50(2): 425-431.

CJ Picard, JD Wells (2012) “A test for carrion fly full siblings: a tool for detecting postmortem relocation of a corpse.”  Journal of Forensic Sciences57(2):535-538.

CJ Picard, JS Johnston, AM Tarone (2012) “Genome sizes of forensically relevant Diptera” Journal of Medical Entomology, 49(1):192-197.

CJ Picard, MH Villet, JD Wells (2012) “Amplified fragment length polymorphism confirms reciprocal monophyly in Chrysomya putoria and Chrysomya chloropyga: a correction of reported shared mtDNA haplotypes”  Medical and Veterinary Entomology, 26: 116-119.

AM Tarone, CJ Picard, C Spieglman, DR Foran (2011) “Population and temperature effects on Lucilia sericata (Diptera: Calliphoridae) body size and minimum development time.” Journal of Medical Entomology, 48(5): 1062-1068.

CJ Picard, JD Wells (2010) “The Population Genetic Structure of North American Lucilia sericata (Diptera: Calliphoridae) and the utility of genetic assignment methods for reconstruction of postmortem corpse relocation.”  Forensic Science International, 195: 63-67.

PB Sampson, CJ Picard, S Handerson, TE McGrath, M Domagala, A Leeson, V Romanov, DE Awrey, D Thambipillai, E Bardounoitis, N Kaplan, JM Berman, HW Pauls  (2009)  “Sprio-Naphthyridinone piperidines as inhibitors of S. aureus and E. coli enoyl-ACP reductase (FabI).”  Bioorganic and Chemistry Letters 19: 5355-5358.

 CJ Picard, JD Wells (2009) “Survey of the Genetic Diversity of Phormia regina (Diptera: Calliphoridae) Using Amplified Fragment Length Polymorphisms.”  Journal of Medical Entomology, 46:664-670.

T Siu, CJ Picard, AK Yudin (2005) “Development of Electrochemical Processes for Nitrene Generation and Transfer.” Journal of Organic Chemistry, 70:932-937.

S Yekta, LB Krasnova, B Mariampillai, CJ Picard, G Chen, S Pandiaraju, AK Yudin (2004) "Preparation and Catalytic Application of Partially Fluorinated Binaphthol Ligands." Journal of Fluorine Chemistry, 125:517-525.

A Caiazzo, S Dalili, CJ Picard, M Sasaki, T Siu, AK Yudin (2004) “New methods for the synthesis of heterocyclic compounds.” Pure & Applied Chemistry, 105:603-613.

 

Book Chapters

CJ Picard, J Whale, J Parrott “Population Genetics and Molecular Evolution of Carrion-Associated Arthropods” in Carrion Ecology, Evolution and Their Applications. In press.

AM Tarone, B Singh, CJ Picard (2015) “Molecular Biology in Forensic Entomology” in International Dimensions and Frontiers in Forensic Entomology. CRC Press.

T Siu, CJ Picard, AK Yudin (2003)  "Electrochemical Nitrogen Transfer Reactions for Organic Synthesis"  In: Mechanistic and Synthetic Aspects of Organic and Biological Electrochemistry, D. G. Peters, J. Simonet, and H. Tanaka, Eds., The Electrochemical Society, Inc., Pennington, New Jersey, pp. 105-108.