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Description
There are several challenges to accurately inferring levels of transcription using RNA-sequencing (RNA-seq) data, including detecting and correcting for reference genome mapping bias. One potential confounder of RNA-seq analysis results from the application of a standardized pipeline to samples of different sexes in species with chromosomal sex determination. The homology

There are several challenges to accurately inferring levels of transcription using RNA-sequencing (RNA-seq) data, including detecting and correcting for reference genome mapping bias. One potential confounder of RNA-seq analysis results from the application of a standardized pipeline to samples of different sexes in species with chromosomal sex determination. The homology between the human X and Y chromosomes will routinely cause mismapping to occur, artificially biasing estimates of sex-biased gene transcription. For this reason we tested sex-specific mapping scenarios in humans on RNA-seq samples from the brains of 5 genetic females and 5 genetic males to assess how inferences of differential gene expression patterns change depending on the reference genome. We first applied a mapping protocol where we mapped all individuals to the entire human reference genome (complete), including the X and Y chromosomes, and computed differential expression between the set of genetic male and genetic female samples. We next mapped the genetic female samples (46,XX) to the human reference genome with the Y chromosome removed (Y-excluded) and the genetic male samples (46, XY) to the human reference genome (including the Y chromosome), but with the pseudoautosomal regions of the Y chromosome hard-masked (YPARs-masked) for the two sex-specific mappings. Using the complete and sex-specific mapping protocols, we compared the differential expression measurements of genetic males and genetic females from cuffDiff outputs. The second strategy called 33 additional genes as being differentially expressed between the two sexes when compared to the complete mapping protocol. This research provides a framework for a new standard of reference genome mappings to correct for sex-biased gene expression estimates that can be used in future studies.
ContributorsBrotman, Sarah Marie (Author) / Wilson Sayres, Melissa (Thesis director) / Crook, Sharon (Committee member) / Webster, Timothy (Committee member) / School of Life Sciences (Contributor) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
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Description
Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to

Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to have evolved from a Y-specific inversion that suppressed recombination across the boundary. In addition to the two PARs, there is also a human-specific X-transposed region (XTR) that was duplicated from the X to the Y chromosome. Genetic diversity is expected to be higher in recombining than nonrecombining regions, particularly because recombination reduces the effects of linked selection, allowing neutral variation to accumulate. We previously showed that diversity decreases linearly across the previously defined pseudoautosomal boundary (rather than drop suddenly at the boundary), suggesting that the pseudoautosomal boundary may not be as strict as previously thought. In this study, we analyzed data from 1271 genetic females to explore the extent to which the pseudoautosomal boundary varies among human populations (broadly, African, European, South Asian, East Asian, and the Americas). We found that, in all populations, genetic diversity was significantly higher in the PAR1 and XTR than in the non-PAR regions, and that diversity decreased linearly from the PAR1 to finally reach a non-PAR value well past the pseudoautosomal boundary in all populations. However, we also found that the location at which diversity changes from reflecting the higher PAR1 diversity to the lower nonPAR diversity varied by as much as 500 kb among populations. The lack of genetic evidence for a strict pseudoautosomal boundary and the variability in patterns of diversity across the pseudoautosomal boundary are consistent with two potential explanations: (1) the boundary itself may vary across populations, or (2) that population-specific demographic histories have shaped diversity across the pseudoautosomal boundary.
ContributorsCotter, Daniel Juetten (Author) / Wilson Sayres, Melissa (Thesis director) / Stone, Anne (Committee member) / Webster, Timothy (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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Description

Medicolegal forensic entomology is the study of insects to aid with legal investigations (Gemmellaro, 2017). Insect evidence can be used to provide information such as the post-mortem interval (PMI). Blow flies are especially useful as these insects are primary colonizers, quickly arriving at a corpse (Malainey & Anderson, 2020). The

Medicolegal forensic entomology is the study of insects to aid with legal investigations (Gemmellaro, 2017). Insect evidence can be used to provide information such as the post-mortem interval (PMI). Blow flies are especially useful as these insects are primary colonizers, quickly arriving at a corpse (Malainey & Anderson, 2020). The age of blow flies found at a scene is used to calculate the PMI. Blow fly age can be estimated using weather data as these insects are poikilothermic (Okpara, 2018). Morphological analysis also can be used to estimate age; however, it is more difficult with pupal samples as the pupae exterior does not change significantly as development progresses (Bala & Sharma, 2016). Gene regulation analysis can estimate the age of samples. MicroRNAs are short noncoding RNA that regulate gene expression (Cannell et al., 2008). Here, we aim to catalog miRNAs expressed during the development of three forensically relevant blow fly species preserved in several storage conditions. Results demonstrated that various miRNA sequences were differentially expressed across pupation. Expression of miR92b increased during mid pupation, aga-miR-92b expression increased during early pupation, and bantam, miR957, and dana-bantam-RA expression increased during late pupation. These results suggest that microRNA can be used to estimate the age of pupal samples as miRNA expression changes throughout pupation. Future work could develop a statistical model to accurately determine age using miRNA expression patterns.

ContributorsHerrera-Quiroz, Demian David (Author) / Parrott, Jonathan (Thesis director) / Weidner, Lauren (Committee member) / School of Mathematical and Natural Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

In this experiment, the viability of gunshot residue (GSR) was examined. This was done through the very rarely researched intersection of forensic firearms analysis and forensic entomology. The question being resolved is if GSR can reliably be detected from secondary evidence transfer of GSR laden carrion onto flies and their

In this experiment, the viability of gunshot residue (GSR) was examined. This was done through the very rarely researched intersection of forensic firearms analysis and forensic entomology. The question being resolved is if GSR can reliably be detected from secondary evidence transfer of GSR laden carrion onto flies and their larvae. While it is know that secondary and tertiary GSR evidence can be transferred by way of handshakes, no such research has been conducted on flies or their pupae. Findings indicated varying levels of detection of GSR on evidence. GSR could reliably be detected on fly bodies and their legs, but not on their pupae. This research is significant as it provides previously unknown information on this line of research and provides the groundwork for further research on this topic in the future.

ContributorsGill, Brendan J (Author) / Parrott, Jonathan (Thesis director) / Weidner, Lauren (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Forensic entomology is an important field of forensic science that utilizes insect evidence in criminal investigations. Blow flies (Diptera: Calliphoridae) are among the first colonizers of remains and are therefore frequently used in determining the minimum postmortem interval (mPMI). Blow fly development, however, is influenced by a variety of factors

Forensic entomology is an important field of forensic science that utilizes insect evidence in criminal investigations. Blow flies (Diptera: Calliphoridae) are among the first colonizers of remains and are therefore frequently used in determining the minimum postmortem interval (mPMI). Blow fly development, however, is influenced by a variety of factors including temperature and feeding substrate type. Unfortunately, dietary fat content remains an understudied factor on the development process, which is problematic given the relatively high rates of obesity in the United States. To study the effects of fat content on blow fly development we investigated the survivorship, adult weight and development of Lucilia sericata (Meigen; Diptera: Calliphoridae) and Phormia regina (Meigen; Diptera: Calliphoridae) on ground beef with a 10%, 20%, or 27% fat content. As fat content increased, survivorship decreased across both species with P. regina being significantly impacted. While P. regina adults were generally larger than L. sericata across all fat levels, only L. sericata demonstrated a significant (P < 0.05) difference in weight by sex. Average total development times for P. regina are comparable to averages published in other literature. Average total development times for L. sericata, however, were nearly 50 hours higher. These findings provide insight on the effect of fat content on blow fly development, a factor that should be considered when estimating a mPMI. By understanding how fat levels affect the survivorship and development of the species studied here, we can begin improving the practice of insect evidence analysis in casework.

ContributorsNoblesse, Andrew (Author) / Weidner, Lauren (Thesis director) / Parrott, Jonathan (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

The field of forensic science has been growing and changing with improvements in DNA analysis. One field affected is forensic entomology, which is exploring many ways in which DNA can increase the application of insects in forensic science. One application being explored is the use of insects as a source

The field of forensic science has been growing and changing with improvements in DNA analysis. One field affected is forensic entomology, which is exploring many ways in which DNA can increase the application of insects in forensic science. One application being explored is the use of insects as a source of human DNA in a criminal investigation. Using flies as a source of foreign DNA can also be utilized in ecological research to conduct surveys on the various species present in different environments. This experiment intends to determine if flies can act as a viable source of alternate DNA. This will be accomplished by an ecological survey of DNA extracted from flies. DNA extractions were performed on flies gathered from parts of the greater Phoenix area. The DNA was then amplified with primers targeting different animal species and examined to observe what animals the flies had come in contact with. Several samples had contamination due to human error and were not able to be evaluated. One DNA extraction out of fifteen yielded pig DNA, indicating flies can be used as a source of DNA. Future experiments should use different animal primers and amplify sections of DNA that can determine the different species consumed by flies. Further research into flies as a DNA source can increase the amount of information available to forensic scientists as well as improve ecologist’s observation of an environment’s biodiversity.

ContributorsRiccomini, Brianna (Author) / Parrott, Jonathan (Thesis director) / Marshall, Pamela (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2023-05
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Description
Forensic entomology is the use of insects in legal investigations, and relies heavily upon calculating the time of colonization (TOC) of insects on remains using temperature-dependent growth rates. If a body is exposed to temperatures that exceed an insect’s critical limit, TOC calculations could be severely affected. The determination of

Forensic entomology is the use of insects in legal investigations, and relies heavily upon calculating the time of colonization (TOC) of insects on remains using temperature-dependent growth rates. If a body is exposed to temperatures that exceed an insect’s critical limit, TOC calculations could be severely affected. The determination of critical thermal limits of forensically-relevant insects is crucial, as their presence or absence could alter the overall postmortem interval (PMI) calculation. This study focuses on the larvae of Phormia regina (Meigen) (Diptera: Calliphoridae), a forensically relevant blow fly common across North America. Three populations were examined (Arizona, Colorado, and New Jersey), and five day old larvae were exposed to one of two temperatures, 39℃ or 45℃, for five hours. Across all colonies, the survival rate was lower at 45℃ than 39℃, in both larval and emerged adult stages. The Arizona colony experienced a harsher drop in survival rates at 45℃ than either the Colorado or New Jersey colonies. This research suggests that the range of 39℃ - 45℃ approaches the critical thermal limit for P. regina, but does not yet exhibit a near or complete failure of survivorship that a critical temperature would cause at this duration of time. However, there is opportunity for further studies to examine this critical temperature by investigating other temperatures within the 39℃ - 45℃ range and at longer durations of time in these temperatures.
ContributorsMcNeil, Tara (Author) / Weidner, Lauren (Thesis director) / Meeds, Andrew (Committee member) / Barrett, The Honors College (Contributor) / School of Humanities, Arts, and Cultural Studies (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2022-05
Description
Previous literature in forensic entomology usually features blow fly research, making literature on forensically relevant beetles hard to find. Although some species of dermestid beetles have been well-studied in regions like Hawaii or the eastern portion of the United States, there has been little forensically focused research regarding dermestid beetles

Previous literature in forensic entomology usually features blow fly research, making literature on forensically relevant beetles hard to find. Although some species of dermestid beetles have been well-studied in regions like Hawaii or the eastern portion of the United States, there has been little forensically focused research regarding dermestid beetles found in the southwestern United States. We were able to report the presence of three species of forensically relevant dermestid beetles on carrion studied in Phoenix, Arizona as well as their relative abundance and wild sex ratios in the spring and summer seasons. Understanding the species of dermestid beetles found in Arizona will aid researchers in determining what beetle species are most important. Knowing the natural sex ratios of commonly found dermestid beetles will be invaluable for optimizing dermestid beetle colony performance for researchers breeding dermestid beetles. The detection of specific species of dermestid beetles will help determine which species of beetles need to be studied first.
ContributorsCromer, Barry (Author) / Weidner, Lauren (Thesis director) / Meeds, Andrew (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2023-12
Description
My Honors Thesis/ Creative Project was an collection of art pieces that were based on a research done at West Campus in Dr. Weidner's forensic entomology laboratory. In this research, two swine carcasses were place outdoors for 21 days during the four seasons. The goal was to collect insects that

My Honors Thesis/ Creative Project was an collection of art pieces that were based on a research done at West Campus in Dr. Weidner's forensic entomology laboratory. In this research, two swine carcasses were place outdoors for 21 days during the four seasons. The goal was to collect insects that approached and colonized the carcasses. The collected data can be used to determine the TOC (time of colonization) of some insects; thus, it can help to calculate the PMI (postmortem interval). Different collection were used like larvae rearing, pitfalls, netting, and hand collection. The larvae were reared into adulthood and then identified into a species. The rest of the insects were identified into orders. To present this information, the data collected from the two carcasses was combined to make the presentation easier to understand. I created four circular canvases to present the collection of flies in each check. It shows both flies were reared and which were seen or collected. The other series of work that I sculpted were 120 ceramics flowers to represent the insects orders that were observed in each season and check. During my thesis defense, I presented the research project, and how my project can help people understand this research.
ContributorsMunoz Zavala, Jaira (Author) / Weidner, Lauren (Thesis director) / Meeds, Andrew (Committee member) / Neubauer, Mary (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Natural Sciences (Contributor) / School of Art (Contributor)
Created2023-12
ContributorsMunoz Zavala, Jaira (Author) / Weidner, Lauren (Thesis director) / Meeds, Andrew (Committee member) / Neubauer, Mary (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Natural Sciences (Contributor) / School of Art (Contributor)
Created2023-12