Browsing by Subject "Phormia regina"

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    Factors Affecting Species Identifications of Blow Fly Pupae Based upon Chemical Profiles and Multivariate Statistics
    (MDPI, 2017-04-11) Kranz, William; Carroll, Clinton; Dixon, Darren A.; Goodpaster, John V.; Picard, Christine J.; Chemistry and Chemical Biology, School of Science
    Alternative methods for the identification of species of blow fly pupae have been developed over the years that consist of the analyses of chemical profiles. However, the effect of biotic and abiotic factors that could influence the predictive manner for the tests have not been evaluated. The lipids of blowfly pupae (Cochliomyia macellaria, Lucilia cuprina, Lucilia sericata, and Phormia regina) were extracted in pentane, derivatized, and analyzed by total-vaporization solid phase microextraction gas chromatography-mass spectrometry (TV-SPME GC-MS). Peak areas for 26 compounds were analyzed. Here we evaluated one biotic factor (colonization) on four species of blow flies to determine how well a model produced from lipid profiles of colonized flies predicted the species of flies of offspring of wild-caught flies and found very good species identification following 10 generations of inbreeding. When we evaluated four abiotic factors in our fly rearing protocols (temperature, humidity, pupation substrate, and diet), we found that the ability to assign the chemical profile to the correct species was greatly reduced.
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    Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research
    (Springer (Biomed Central Ltd.), 2016-10-28) Andere, Anne A.; Platt, Roy N.; Ray, David A.; Picard, Christine J.; Department of Biology, School of Science
    BACKGROUND: Blow flies (Diptera: Calliphoridae) are important medical, veterinary and forensic insects encompassing 8 % of the species diversity observed in the calyptrate insects. Few genomic resources exist to understand the diversity and evolution of this group. RESULTS: We present the hybrid (short and long reads) draft assemblies of the male and female genomes of the common North American blow fly, Phormia regina (Diptera: Calliphoridae). The 550 and 534 Mb draft assemblies contained 8312 and 9490 predicted genes in the female and male genomes, respectively; including > 93 % conserved eukaryotic genes. Putative X and Y chromosomes (21 and 14 Mb, respectively) were assembled and annotated. The P. regina genomes appear to contain few mobile genetic elements, an almost complete absence of SINEs, and most of the repetitive landscape consists of simple repetitive sequences. Candidate gene approaches were undertaken to annotate insecticide resistance, sex-determining, chemoreceptors, and antimicrobial peptides. CONCLUSIONS: This work yielded a robust, reliable reference calliphorid genome from a species located in the middle of a calliphorid phylogeny. By adding an additional blow fly genome, the ability to tease apart what might be true of general calliphorids vs. what is specific of two distinct lineages now exists. This resource will provide a strong foundation for future studies into the evolution, population structure, behavior, and physiology of all blow flies.
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    De Novo Genome Assembly of Phormia regina (Diptera: Calliphoridae)
    (Office of the Vice Chancellor for Research, 2014-04-11) Andere, Anne A.; Picard, Christine J.
    Phormia regina (Meigen), commonly known as the black blow fly, is a dipteran that belongs to the family Calliphoridae (blow flies). Calliphorids play an important role in various research fields like ecology, medical studies, veterinary and forensic sciences. P. regina is one of the common forensically relevant insects in North America and is typically used to assist in estimating post-mortem intervals (PMI). To better understand the roles it plays in the numerous research fields, we aim to re-construct its genome using next generation sequencing technologies. We are specifically focusing on generating a reference genome by de novo assembly then use the genomic data to identify genetic markers (microsatellites, single nucleotide polymorphisms) that contribute to intra- and inter-population variation with regards to geographic location. DNA was extracted from five adult male and female flies and was sequenced using the Illumina HiSeq2000 sequencing platform. More than 250 million high quality reads were produced from each sex. These reads were used in the de novo genome assembly of the female, male and combined sexes. The assembled draft genomes produced approximately 251,115 contigs, 306,273 contigs, and 325,664 contigs respectively. The assembled genome sizes totaled to ~524 Mbp and ~508 Mbp for the female and male flies, respectively. Compared to the estimated genome sizes from a previous study of 529 Mbp for females and 517 Mbp for males, we can conclude that a majority of the genome sequence (~99%) is included in the assembly. Gene prediction and annotation of the draft genomes are currently in progress. The draft reference genomes assembled from this study will provide an important resource for analyzing genetic basis of variations between and among blow fly species, which will ultimately facilitate ongoing studies in various areas of research that utilize blow flies as study models. It will also be a source where reliable genomic data can be readily available and used in downstream analysis to increase the understanding of the genetic, molecular and cellular processes of blow flies.
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    Optimization of total vaporization solid-phase microextraction (TV-SPME) for the determination of lipid profiles of Phormia regina, a forensically important blow fly species
    (Springer, 2017-11) Kranz, William; Carroll, Clinton; Dixon, Darren; Picard, Christine J.; Goodpaster, John V.; Chemistry and Chemical Biology, School of Science
    A new method has been developed for the determination of fatty acids, sterols, and other lipids which naturally occur within pupae of the blow fly Phormia regina. The method relies upon liquid extraction in non-polar solvent, followed by derivatization using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) w/ 1% trimethylchlorsilane (TMCS) carried out inside the sample vial. The analysis is facilitated by total vaporization solid-phase microextraction (TV-SPME), with gas chromatography-mass spectrometry (GC-MS) serving as the instrumentation for analysis. The TV-SPME delivery technique is approximately a factor of five more sensitive than traditional liquid injection, which may alleviate the need for rotary evaporation, reconstitution, collection of high performance liquid chromatography fractions, and many of the other pre-concentration steps that are commonplace in the current literature. Furthermore, the ability to derivatize the liquid extract in a single easy step while increasing sensitivity represents an improvement over current derivatization methods. The most common lipids identified in fly pupae were various saturated and unsaturated fatty acids ranging from lauric acid (12:0) to arachinoic acid (20:4), as well as cholesterol. The concentrations of myristic acid (14:0), palmitelaidic acid (16:2), and palmitoleic acid (16:1) were the most reliable indicators of the age of the pupae.
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    Population Genetics of the blow fly Phormia regina (Meigen)
    (Office of the Vice Chancellor for Research, 2014-04-11) Whale, John W.; Picard, Christine J.
    Blow flies (Diptera: Calliphoridae) are a family of flies which are associated with the decomposition of organic matter, and the many species are widely distributed across the globe inhabiting almost every ecosystem and continent, with the exception being Antarctica. For many years, biologists have been interested in these metamorphic insects with much attention in recent years with their predictable life cycle and subsequent application in death investigations. Phormia regina (Meigen) is a primary colonizer of carrion and is widely distributed across the United States and can be found throughout the year. Recently, molecular techniques have been applied to a number of blow fly species, initially for identification purposes to corroborate morphological taxonomy but also as an alternative to morphology when specimens are damaged. Even more recently, population structure of these flies have been investigated, however these studies have primarily focused on pest species which infest living livestock and directly affect the agricultural economy. Here, we build upon previous analysis with AFLP markers on P. regina to determine the population structure of this integral species by using tetra-nucleotide microsatellite markers. From the recently constructed draft genome of P. regina, several thousand tetra-nucleotide (four-base repeating sequences of DNA) were identified. Due to the high A-T content of insect DNA, repeats consisting wholly of adenine and thymine bases were discarded. From the remaining tetra-repeats, 14 were chosen for initial analysis to determine their polymorphic nature; from here six were selected for genotypic analysis. More than 200 different P. regina individuals belonging to 27 populations collected from across the contiguous United States have been genotyped across these six tetra-nucleotide loci. Five loci possess ≥30 different alleles, while the sixth appears to be fairly conserved with eight different alleles. Heterozygosity exhibited between these populations is uniform (0.5-0.8) while inbred lab colonies exhibit an increase in homozygosity from their ancestral population. Further analyses are to be performed in order to determine the population structure and geography-genetic relationships of these flies.
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    Utilizing Phormia Regina as an Environmental Sensor for Resource Identification and Biodiversity Monitoring
    (2024-08) Jensen, Katharine Theresa; Picard, Christine; Manicke, Nicholas; Dembinski, Gina
    Blow flies are a family of carrion insects that are among the first to arrive in the decomposition process. Blow flies are known to ingest carrion, feces, water, and occasionally nectar to meet nutritional requirements. These behaviors make blow flies a unique organism potentially containing genetic material from a variety of sources within one environment. Their global distribution and ease of capture makes them a strong candidate for resource monitoring and identification. While previous studies have evaluated the suitability of blow flies for vertebrate biodiversity estimates, no work has been done looking at their ability to ingest and store genetic material from plants and microbes present in water. It is also not known how long these DNA signals persist in the gut. Through DNA analysis of the blow fly gut, researchers can identify vertebrates that have recently died in an environment, what plant species are present, and what water source the insect utilized. Through lab colony (Phormia regina) feeding experiments, it was determined that at 25 ˚C and 50 % relative humidity, vertebrate and plant DNA persist in the gut for over 120 hours post-ingestion. Wild sample analysis of flies collected from Yellowstone National Park was performed to identify plant species ingested by P. regina in the wild. Following Sanger sequencing, top hits on BLASTn included Brassicales, Juglans cathyensis, and uncultured Candida. This is the first application of environmental DNA analysis techniques to insects for the purpose of plant identification. This work also attempts to characterize microbial profiles of the gut of P. regina for the purpose of water resource identification. Over a two-month collection period, samples were collected from different water resources across Indianapolis. Flies were exposed to these samples in a controlled feeding experiment, followed by sampling at 0- and 72 hours post-exposure. Gut samples were sequenced using Illumina and Operational Taxonomic Unit clustering grouped reads by sequence similarity for identification. Bacteria classes identified included Gammaproteobacteria, Bacteroidia, Flavobacteria, Alphaproteobacteria, Bacilli, Clostridia, Actinobacteria, Betaproteobacteria, and Fusobacteria. Many bacteria classes were common across water samples, although the abundance of each class changed between samples and across time. These unique microbial profiles can be used to identify water resources for potential contamination and chemical dumping. Further work is necessary to generate microbial profiles from the original water sources themselves and for generation of alpha and beta diversities. Overall, this work spans multiple fields. Species identification is important for biodiversity monitoring and environmental surveys. Utilizing blow fly derived DNA allows for detection of living and deceased vertebrates in an environment, plant life, and water quality within one sample. This work also has implications in forensic science, specifically wildlife forensics and chemical detection of clandestine laboratories and chemical weapon compounds.