IU Indianapolis ScholarWorks :: Browsing by Author "Picard, Christine J."

Browsing by Author "Picard, Christine J."

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A Reference Database for the DNA-Based Identification of North American Calliphorinae
(North American Forensic Entomological Association (NAFEA), 2023) Picard, Christine J.; Balaji, Adhitya; Benson, Diamond
DNA-based species identifications are a robust tool for the forensic entomologist to identify immature or damaged specimens to species or genus taxonomic levels for further forensic analyses. However, much of that identification is dependent on the use of a reliable database that encompasses all species possible for a given geographic area. Here, we queried databases for DNA records of COI sequence data of 18 species of Calliphorinae present in North America to determine the applicability and reliability of DNA-based identifications, and to provide a resource for the community. Our results indicate that approximately 650bp of the standard DNA barcode is sufficient to classify most Calliphorinae species, however, some species the ~650bp COI barcode is insufficient to resolve to species for the North American Calliphorinae subfamily. We tested this reference dataset by selecting records that were deemed reliable (using the same criteria as establishing the reference dataset) to test the accuracy of the identifications based on DNA COI sequences and found that all test specimens were accurately identified except for the two paraphyletic species present in the dataset. We furthermore state what species can and cannot be reliably classified and provide guidance on using this database in future applications.
Amplified fragment length polymorphism analysis supports the valid separate species status of Lucilia caesar and L. illustris (Diptera: Calliphoridae)
(Taylor & Francis:, 2017-12-08) Picard, Christine J.; Wells, Jeffrey D.; Ullyot, Anne; Rognes, Knut; Biology, School of Science
Common DNA-based species determination methods fail to distinguish some blow flies in the forensically and medically important genus Lucilia Robineau-Desvoidy. This is a practical problem, and it has also been interpreted as casting doubt on the validity of some morphologically defined species. An example is Lucilia illustris and L. caesar, which co-occur in Europe whilst only L. illustris has been collected in North America. Reports that these species shared both mitochondrial and nuclear gene sequences, along with claims that diagnostic morphological characters are difficult to interpret, were used to question their separate species status. We report here that amplified fragment length polymorphism profiles strongly support the validity of both species based on both assignment and phylogenetic analysis, and that traditional identification criteria based on male and female genital morphology are more reliable than has been claimed.
Blow fly stable isotopes reveal larval diet: A case study in community level anthropogenic effects
(PLOS, 2021-04) Owings, Charity G.; Gilhooly, William P. III; Picard, Christine J.; Earth Sciences, School of Science
Response to human impacts on the environment are typically initiated too late to remediate negative consequences. We present the novel use of stable isotope analysis (SIA) of blow flies to determine human influences on vertebrate communities in a range of human-inhabited environments, from a pristine national park to a dense metropolitan area. The refrain “you are what you eat” applies to the dietary isotope record of all living organisms, and for carrion-breeding blow flies, this translates to the type of carcasses present in an environment. Specifically, we show that carnivore carcasses make up a large proportion of the adult fly’s prior larval diet, which contrasts to what has been reportedly previously for the wild adult fly diet (which consists of mostly herbivore resources). Additionally, we reveal the potential impact of human food on carcasses that were fed on by blow flies, underscoring the human influences on wild animal populations. Our results demonstrate that using SIA in conjunction with other methods (e.g., DNA analysis of flies) can reveal a comprehensive snapshot of the vertebrate community in a terrestrial ecosystem.
Characterizing Femoral Structure of the Ts66Yah Mouse Model of Down Syndrome
(2023-08) Sloan, Kourtney; Roper, Randall J.; Li, Jiliang; McNulty, Margaret A.; Picard, Christine J.
Down syndrome (DS) is caused by the partial or complete trisomy of human chromosome 21 (Hsa21) and can result in skeletal deficits, including lower bone mineral density (BMD) and increased risk of fracture and osteoporosis or osteopenia earlier than the general population. Mouse models of DS have been developed to understand the genetic mechanisms resulting in these phenotypes, but models differ due to the complex genetic nature of DS and differing genome structures between humans and mice. Ts65Dn mice have been a popular model of DS as they contain ~50% of Hsa21 orthologous genes on a freely segregating minichromosome, but there is speculation that the phenotypes are exaggerated by non-Hsa21 orthologous trisomic genes also present. To address this issue, the Ts66Yah mouse model was developed to remove the non-Hsa21 orthologous trisomic genes. In this study, male and female Ts66Yah mouse femurs were evaluated during bone accrual and peak bone mass to investigate structural differences using micro-computed tomography. Additionally, the role of trisomic Dyrk1a, a Hsa21 gene previously linked to bone deficits in Ts65Dn mice, was evaluated through genetic and pharmacological means in Ts66Yah femurs at postnatal day 36. Ts66Yah mice were found to have little or no trabecular deficits at any age evaluated, but sex-dependent cortical deficits were present at all ages investigated. Reducing Dyrk1a copy number in Ts66Yah mice significantly improved cortical deficits but did not return cortical bone to euploid levels. Pharmacological treatment with DYRK1A inhibitor L21 was confounded by multiple variables, making it difficult to draw conclusions about DYRK1A inhibition in this manner. Overall, these results indicate trabecular deficits associated with Ts65Dn mice may be due to the non-Hsa21 orthologous trisomic genes, and more Hsa21 orthologous trisomic genes are necessary to produce trabecular deficits in DS model mice. As more mouse models of DS are developed, multiple models need to be assessed to accurately define DS-associated phenotypes and test potential treatments.
Chemical Assay for the Detection of Vertebrate Fecal Metabolites in Adult Blow Flies (Diptera: Calliphoridae)
(Oxford, 2018-06-06) Owings, Charity G.; Skaggs, Christine; Sheriff, Winyu; Manicke, Nicholas; Picard, Christine J.; Department of Biology, School of Science
Filth flies are commonly implicated in pathogen transmission routes due to their affinity for vertebrate waste and their synanthropic associations. However, solidifying the link between flies and infected feces in the wild can be difficult, as interpretations made solely from microbial culturing or sequencing methods may represent an incomplete picture of pathogen acquisition. We present an analytical assay using high performance liquid chromatography tandem mass spectrometry (HPLC MS/MS) to detect vertebrate fecal metabolites (urobilinoids) in adult blow fly guts. Proof of concept experiments consisted of controlled feeding in which flies were grouped into three treatments (unfed, exposure to beef liver tissue, and exposure to canine feces; N = 20/treatment) using the black blow fly Phormia regina Meigen (Diptera: Calliphoridae). It was revealed that only feces-related samples exhibited peaks with an m/z of 591 and MS/MS spectra consistent with urobilinoids. These peaks were not seen for beef liver tissue, flies exposed to beef liver tissue, or unfed flies. Samples taken directly from beef liver tissue and from feces of several animals were also tested. To test this assay in wild flies, 216 flies were additionally analyzed to determine whether they had ingested vertebrate feces. About 13% of the wild flies exhibited these same peaks, providing a baseline measure of blow flies collected in urban and residential areas consuming feces from the environment. Overall, this assay can be used for P. regina collected in an applied setting and its integration with microbial culturing and sequencing methods will help to improve its use.
Classifying the Unknown: Identification of Insects by Deep Open-set Bayesian Learning
(bioRxiv, 2021-09-17) Badirli, Sarkhan; Picard, Christine J.; Mohler, George; Akata, Zeynep; Dundar, Murat
Insects represent a large majority of biodiversity on Earth, yet only 20% of the estimated 5.5 million insect species are currently described (1). While describing new species typically requires specific taxonomic expertise to identify morphological characters that distinguish it from other potential species, DNA-based methods have aided in providing additional evidence of separate species (2). Machine learning (ML) is emerging as a potential new approach in identifying new species, given that this analysis may be more sensitive to subtle differences humans may not process. Existing ML algorithms are limited by image repositories that do not include undescribed species. We developed a Bayesian deep learning method for the open-set classification of species. The proposed approach forms a Bayesian hierarchy of species around corresponding genera and uses deep embeddings of images and barcodes together to identify insects at the lowest level of abstraction possible. To demonstrate proof of concept, we used a database of 32,848 insect instances from 1,040 described species split into training and test data. The test data included 243 species not present in the training data. Our results demonstrate that using DNA sequences and images together, insect instances of described species can be classified with 96.66% accuracy while achieving accuracy of 81.39% in identifying genera of insect instances of undescribed species. The proposed deep open-set Bayesian model demonstrates a powerful new approach that can be used for the gargantuan task of identifying new insect species.
Comparative genomics of the sheep blow fly Lucilia cuprina
(Office of the Vice Chancellor for Research, 2016-04-08) Picard, Christine J.; Andere, Anne A.
Insects employ different adaptive strategies in response to selective pressures, such as competition for limited resources. Carrion insects provide the ideal case to study these fundamental processes of adaptive evolution due to the intense selective pressures placed on developing larvae with limited food resources, their widespread and abundant distributions, and the presence of geographically distinct populations with specialized adaptations. One adaptation is facultative ectoparasitism, where the insect strikes a healthy animal and feeds on the living flesh, providing a developmental advantage over competitor fly species, but causing significant harm to the host. Lucilia species, which hybridize in the wild and form geographically distinct subpopulations in other regions, are diverging, meaning that we can observe and quantify early biological adaptive processes that govern speciation as they are occurring over hundreds, instead of millions, of years. The draft genome of a North American male Lucilia cuprina fly (carrion breeder) was assembled using a combination of short and long read sequences. This genome is compared to an existing Australian draft genome (ectoparasite) by elucidating genomic structure in key adaptive processes (i.e. immune system evasion) via high-throughput re-sequencing of parasitic specimens, gene prediction and annotation. The carcass colonized by or animal parasitized by both species, with some geographic overlap, provides a semi-controlled environment within the larger context of the ecosystem to sample a large number of individuals with similar life history strategies, allowing for direct comparative studies to elucidate the correlation between structure and function in the genomes of carrion flies – allowing us to understand biological adaptation and speciation.
Detection and Quantification of Taste and Odor Producing Bacteria in Eagle Creek Reservoir
(2019-08) Koltsidou, Ioanna; Picard, Christine J.; Druschel, Gregory K.; Anderson, Gregory G.
The accelerated growth of algal blooms in water bodies has caused the increased occurrence of taste and odor (T&O) episodes worldwide. Even though T&O compounds have not been associated with adverse health effects, their presence can have extensive socio-economic impacts in contaminated waters. Eagle Creek Reservoir, a eutrophic water body, which supplies about 80% of Indianapolis drinking water, experiences frequent and sometimes severe odorous outbreaks. The terpenoid bacterial metabolites, 2-methylisoborneol (2-MIB) and geosmin, have been identified as the main compounds contributing to those T&O problems, which occur seasonally when the reservoir receives most of its water and nutrient loads from discharge events. In this study, ECR’s microbial community composition was assessed by a 16S next generation sequencing approach, confirming the presence of the major bacterial phyla of Cyanobacteria, Proteobacteria, Actinobacteria and Bacteroidetes, which are commonly found in freshwater environments. The relative abundance of Cyanobacteria, which are regarded as the main T&O producers in freshwater, followed the fluctuation of 2-MIB and geosmin concentrations closely. Mapping sequence analysis of a metagenomic dataset, successfully recovered the genes responsible for the synthesis of geosmin and 2-MIB, demonstrating the microbial ability for odorous compound production in ECR. Quantification of the geoA and MIBS genes in Cyanobacteria was achieved by the development and application of qPCR assays on water samples collected from the reservoir. A statistically significant positive correlation was found between MIBS gene quantity and MIB concentration for all sampling locations, implying that this assay could potentially be used as a tool for the early prediction of upcoming T&O episodes. The geoA gene detection assay, did not correlate well with geosmin concentrations, suggesting that even though the gene might be present, this does not necessarily mean that it is metabolically active.
Estimation of the number of contributors of theoretical mixture profiles based on allele counting: Does increasing the number of loci increase success rate of estimates?
(Elsevier, 2018-03) Dembinski, Gina M.; Sobieralski, Carl; Picard, Christine J.; Biology, School of Science
DNA mixtures are more frequently encountered in casework due to increased kit sensitivity, protocols with increased cycle number, and requests for low copy number DNA samples to be tested. Generally, the first step in mixture interpretation is determining the number of contributors, with the most common approach of maximum allele count. Although there are previous studies regarding the accuracy of this approach, none have evaluated the accuracy with the newly expanded U.S. core STR loci. In this work, 4,976,355 theoretical mixture combinations were generated with the PowerPlex® Fusion 6C system which includes 23 autosomal STR loci and three Y-STR loci. The number of contributors could be correctly assumed for 100% two-person and 99.99% three-person mixtures, whereas, four-, five-, and six-person mixtures were correctly assumed in 89.7%, 57.3%, and 7.8% of mixtures, respectively. Y-STR analysis showed the 3 Y-STR markers are only accurate for two-person male mixtures (96.7%). This work demonstrates that maximum allele count using the expanded U.S. core loci is not much improved from previous smaller panels, reiterating that this method is not as accurate beyond three contributors.
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.

Browsing by Author "Picard, Christine J."

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