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P08. Unravelling Organelle Genome Evolution Architecture Using Rna-Sequencing Data, Matheus Sanita Lima, David Roy Smith 2017 Western University

P08. Unravelling Organelle Genome Evolution Architecture Using Rna-Sequencing Data, Matheus Sanita Lima, David Roy Smith

Western Research Forum

Background: Mitochondria genomes vary from 11 Mb to 6 kb, while plastids can vary from 1 Mb to 30 kb. Non-coding DNA accounts for most of this size variation, but the mechanistic and evolutionary reasons for that are still unknown. Next generation sequencing has generated unprecedented amounts of genomic and transcriptomic data that can be used for organelle genome evolution studies. However, most of these data is used only for the study of cell nucleus. Therefore, I decided to use these untapped data source to investigate the transcription of organelle genomes in plastid-bearing protists.

Methods: I mapped the transcriptomes over ...


Blood Mercury Levels Of Zebra Finches Are Heritable: Implications For The Evolution Of Mercury Resistance, Kenton A. Buck, Claire W. Varian-Ramos, Daniel A. Cristol, John P. Swaddle 2017 College of William and Mary

Blood Mercury Levels Of Zebra Finches Are Heritable: Implications For The Evolution Of Mercury Resistance, Kenton A. Buck, Claire W. Varian-Ramos, Daniel A. Cristol, John P. Swaddle

John Swaddle

Mercury is a ubiquitous metal contaminant that negatively impacts reproduction of wildlife and has many other sub-lethal effects. Songbirds are sensitive bioindicators of mercury toxicity and may suffer population declines as a result of mercury pollution. Current predictions of mercury accumulation and biomagnification often overlook possible genetic variation in mercury uptake and elimination within species and the potential for evolution in affected populations. We conducted a study of dietary mercury exposure in a model songbird species, maintaining a breeding population of zebra finches (Taeniopygia guttata) on standardized diets ranging from 0.0–2.4 μg/g methylmercury. We applied a ...


Genetic Architecture And Predictability Of Seedling Root Traits In Maize (Zea Mays L.), Jordon Michael Pace 2017 Iowa State University

Genetic Architecture And Predictability Of Seedling Root Traits In Maize (Zea Mays L.), Jordon Michael Pace

Michael Pace

The maize (Zea mays L.) root system is important for proper growth and productivity of the plant. There is substantial genetic and phenotypic variation for root architecture, which gives opportunity for selection. Root traits, however, have not been used as selection criterion mainly due to the difficulty in measuring, as well as their quantitative mode of inheritance. Studying seedling roots offer an opportunity to study multiple individuals and to enable repeated measurements per year as compared to adult root phenotyping. Here we have evaluated phenotypic and genotypic variation within seedling root traits for two panels of inbred lines. Constructed maize ...


Mhc Class Iiβ Diversity As A Correlate Of Neutral-Locus Similarity And Diversity, And A Predictor Of Overwinter Return, In Song Sparrows (Melospiza Melodia), Matthew J. Watson 2017 The University of Western Ontario

Mhc Class Iiβ Diversity As A Correlate Of Neutral-Locus Similarity And Diversity, And A Predictor Of Overwinter Return, In Song Sparrows (Melospiza Melodia), Matthew J. Watson

Electronic Thesis and Dissertation Repository

Abstract

The major histocompatibility complex (MHC) is a family of genes involved with recognizing pathogens and mounting an immune response. Parasite-mediated selection often favours heterozygosity at MHC because MHC-diverse individuals recognize a wider range of pathogens. Because migratory birds encounter many pathogens, I hypothesized that MHC diversity predicts overwinter and juvenile survivorship in song sparrows (Melospiza melodia). I found no correlation between MHC diversity and neutral-locus (microsatellite) heterozygosity, suggesting that measures of neutral and adaptive genetic diversity provide complementary rather than redundant information. However, pairwise similarity at MHC predicted pairwise similarity at microsatellite loci. In contrast to my hypothesis, MHC ...


Hypoxia Inducible Factor 1: A Urinary Biomarker Of Kidney Disease., S Movafagh, Dominic Raj, M Sanaei-Ardekani, D Bhatia, K Vo, M Mahmoudieh, R Rahman, E H Kim, Arthur F Harralson 2017 George Washington University

Hypoxia Inducible Factor 1: A Urinary Biomarker Of Kidney Disease., S Movafagh, Dominic Raj, M Sanaei-Ardekani, D Bhatia, K Vo, M Mahmoudieh, R Rahman, E H Kim, Arthur F Harralson

Medicine Faculty Publications

Identifying noninvasive biomarkers of kidney disease is valuable for diagnostic and therapeutic purposes. Hypoxia inducible factor 1 (HIF-1) expression is known to be elevated in the kidneys in several renal disease pathologies. We hypothesized that the urinary HIF-1a mRNA level may be a suitable biomarker for expression of this protein in chronic kidney disease (CKD). We compared HIF-1a mRNA levels from urine pellets of CKD and healthy subjects. To ensure that urinary HIF-1a mRNA is of kidney origin, we examined colocalization of HIF-1a mRNA with two kidney specific markers in urine cells. We found that HIF-1a mRNA is readily quantifiable ...


Microbial Repopulation Following In Situ Star Remediation, Gavin Overbeeke 2017 The University of Western Ontario

Microbial Repopulation Following In Situ Star Remediation, Gavin Overbeeke

Electronic Thesis and Dissertation Repository

In situ STAR (Self-sustaining Treatment for Active Remediation) is an emerging remediation technology which uses smouldering combustion to destroy nonaqueous phase liquid (NAPL) contamination in the subsurface. Since STAR smouldering travels through contaminated soils slowly (~0.5 to 5 m/day) and subjects them to high temperatures (400–1000°C), it is expected that this technology will thoroughly dry and sterilize the zones which it treats. Further, soils surrounding the treatment zone which are not smouldered will be heated, although not smouldered, by virtue of their proximity to STAR, impacting microbial communities within them. Therefore, the objectives of this work ...


Human-Nonhuman Chimeras, Ontology, And Dignity: A Constructivist Approach To The Ethics Of Conducting Research On Cross-Species Hybrids, Jonathan M. Vajda 2017 Western Michigan University

Human-Nonhuman Chimeras, Ontology, And Dignity: A Constructivist Approach To The Ethics Of Conducting Research On Cross-Species Hybrids, Jonathan M. Vajda

The Hilltop Review

Developments in biological technology in the last few decades highlight the surprising and ever-expanding practical benefits of stem cells. With this progress, the possibility of combining human and nonhuman organisms is a reality, with ethical boundaries that are not readily obvious. These inter-species hybrids are of a larger class of biological entities called “chimeras.” As the concept of a human-nonhuman creature is conjured in our minds, either incredulous wonder or grotesque horror is likely to follow. This paper seeks to mitigate those worries and demotivate reasonable concerns raised against chimera research, all the while pressing current ethical positions toward their ...


A Rare Breed: Wild-Type Braf And Ighv Expression In A 29 Year Old Lady With Classical Hairy Cell Leukemia, A. Hossain, Hind Rafei, Amar Jariwala, Khaled El-Shami 2017 George Washington University

A Rare Breed: Wild-Type Braf And Ighv Expression In A 29 Year Old Lady With Classical Hairy Cell Leukemia, A. Hossain, Hind Rafei, Amar Jariwala, Khaled El-Shami

Medicine Faculty Publications

The V600 BRAF mutation has been described as a key mutation in the pathogenesis of classical hairy cell leukemia (c-HCL) cases without expression of a mutant immunoglobulin heavy chain (IgHV). Here we present a rare case of c-HCL with neither V600 BRAF mutation nor the aforementioned IgHV variant successfully treated with cladribine and review the current literature on its use in women of childbearing age/pregnancy.


Sequence-Based Prediction Of Rna-Binding Residues In Proteins, Rasna R. Walia, Yasser EL-Manzalawy, Vasant G. Honavar, Drena Dobbs 2017 United States Department of Agriculture

Sequence-Based Prediction Of Rna-Binding Residues In Proteins, Rasna R. Walia, Yasser El-Manzalawy, Vasant G. Honavar, Drena Dobbs

Genetics, Development and Cell Biology Publications

Identifying individual residues in the interfaces of protein–RNA complexes is important for understanding the molecular determinants of protein–RNA recognition and has many potential applications. Recent technical advances have led to several high-throughput experimental methods for identifying partners in protein–RNA complexes, but determining RNA-binding residues in proteins is still expensive and time-consuming. This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate directly in contacting RNA. Step-by-step protocols for using three different web-based servers to predict RNA-binding residues are described. In addition, currently available web servers and software tools for predicting ...


Genetic Basis Of Resistance To Avian Influenza, Wioleta Drobik-Czwarno, Janet Fulton, Jesus Arango, Petek Settar, Anna Wolc, Jack C. M. Dekkers 2017 Warsaw University of Life Sciences

Genetic Basis Of Resistance To Avian Influenza, Wioleta Drobik-Czwarno, Janet Fulton, Jesus Arango, Petek Settar, Anna Wolc, Jack C. M. Dekkers

Animal Industry Report

Two high pathogenic avian influenza (HPAI) outbreaks haveseverelyaffected the poultry industryon the American continentwithin the last four years; a 2012 H7N3 outbreak in Mexicoand a 2015 H5N2 outbreak in the US. Blood samples were collectedfrom survivors of each outbreak plus age and genetics matched non-affected controls. As surviving birds could contain natural genetic mutation(s) that make them resistant to HPAI,the goal of the present study was to identify genomic regions associated with resistance to HPAIand to determinewhether resistance regionsare the same fordifferent virus strains.Four genomic regions were identified for the H5N2 outbreak and fivedifferent regions were identified ...


Egg Shell Quality Assessment–Do We Need Multiple Records?, Anna Wolc, Jesus Arango, Petek Settar, Neil P. O'Sullivan, Jack C. M. Dekkers 2017 Iowa State University

Egg Shell Quality Assessment–Do We Need Multiple Records?, Anna Wolc, Jesus Arango, Petek Settar, Neil P. O'Sullivan, Jack C. M. Dekkers

Animal Industry Report

The objective of this study was to estimate repeatability within and between ages for dynamic stiffnessin two lines of layer chickens in order to verify if multiple records are necessary to adequately describe a bird’s genetic merit for egg shell quality.Repeatability was low across ages to moderate within age,which suggests that for accurate evaluation eggs should be collected at different stages of laying cycle,with additional benefit from analyzing more than one egg within age.


The Effect Of Prrs Viral Level And Isolate On Tonsil Gene Expression, Qian Dong, Joan Lunney, Elyn Fritz-Waters, Yet Nguyen, Bob Rowland, Andrew Hess, James Reecy, Jack Dekkers 2017 Iowa State University

The Effect Of Prrs Viral Level And Isolate On Tonsil Gene Expression, Qian Dong, Joan Lunney, Elyn Fritz-Waters, Yet Nguyen, Bob Rowland, Andrew Hess, James Reecy, Jack Dekkers

Animal Industry Report

Porcine Reproductive and Respiratory Syndrome virus (PRRSV) can persist in tonsil tissue for >150 days post infection (dpi) without clinical signs.This can occur even when PRRSV is cleared from serumand can result insecondary outbreaks. Tonsil tissue from commercial crossbred pigs that were experimentally infected with one of two PRRSV isolates, NVSL-97-7985 (NVSL) or KS-2006-72109 (KS06),was used to identify genes that were differentially expressed in pigs with extreme high or low tonsil PRRS viremia at 42 dpi. Results provide insighton the mechanisms of PRRSV persistence in tonsils and help to identify bio-markers for PRRSV persistence in tonsil tissue.This ...


Effects Of Diet And Genetics On Production Traits In Response To Repeated Exposure To Heat Stress In Pigs, Wendy Rauw, Johana Mayorga Lozano, Soi Lei, John Patience, Nicholas Gabler, Steven Lonergan, Jack Dekkers, Lance Baumgard 2017 Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

Effects Of Diet And Genetics On Production Traits In Response To Repeated Exposure To Heat Stress In Pigs, Wendy Rauw, Johana Mayorga Lozano, Soi Lei, John Patience, Nicholas Gabler, Steven Lonergan, Jack Dekkers, Lance Baumgard

Animal Industry Report

Hot temperatures negatively impact global livestock production and are a serious financial burden to pig producers. Trends predict that global temperatures will continue toincrease, making this a pertinent issue now and in the future. Study objectives were to investigate the effects of genetics and dietary fiber content on growth,feed intake, and feed conversion efficiencyin response to repeated exposure to heat stress.Atotal of 103 finishing barrows from a contemporary commercial line and Yorkshire linesdivergently selected for high and low feed efficiency based on residual feed intake (RFI) were used in this experiment. All pigs were subjected three consecutivetimes to ...


Evaluation Of Serum Viremia Of Pigs With Alternate Genotypes For A Major Gene After Natural Prrsv Infection On A Commercial Farm, Luis Gomez-Raya, Jenelle Dunkelberger, Joan Lunney, Raymond Robert R. Rowland, Jack Dekkers 2017 Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

Evaluation Of Serum Viremia Of Pigs With Alternate Genotypes For A Major Gene After Natural Prrsv Infection On A Commercial Farm, Luis Gomez-Raya, Jenelle Dunkelberger, Joan Lunney, Raymond Robert R. Rowland, Jack Dekkers

Animal Industry Report

The objective of this study was to investigate alternative measures to evaluate serum viremiaafternatural Porcine Reproductive and Respiratory SyndromeVirus (PRRSV)infection of pigs on a commercial farm. Viremia measurements (area under the curve at 21 days from the startof the trial, maximum viremia, time to maximum viremia, and ratioof maximum viremia over time to maximum viremia) were estimated using a LOESSfunction for each animal. Genetic markerWUR10000125 (WUR)on chromosome 4 was typedfor 199 barrowsand its association with viremia traits was tested.The analysis revealedthat maximum viremia wassignificantly(P<0.01)lower for pigs with the AB genotype. Maximum viremia canbe used as the indicator trait of the severity of the infection in commercial farms where animalsdiffer in the time of the initial infection.


Exploration Of Dna Transfer In The Nyc Subway, Sannia K. Tauqeer 2016 CUNY John Jay College

Exploration Of Dna Transfer In The Nyc Subway, Sannia K. Tauqeer

Student Theses

The ability to detect “touch” DNA has complicated the interpretation of DNA profiles in the field of forensics because it leads to the introduction of the concept of DNA transfer, persistence and background into casework. This project is geared towards understanding DNA transfer in the NYC subways and has relevance in groping and attempted sexual assault cases, where garments are submitted as evidence. The study involved 10 volunteers who were asked to wear a clean jacket during their trips on the subway for one week and the DNA from these jackets was collected, extracted, quantified, amplified and typed. The results ...


Evolution In Light Of Mitonuclear Landscapes An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), Stephen D. Flanagan 2016 University of Southern Mississippi

Evolution In Light Of Mitonuclear Landscapes An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), Stephen D. Flanagan

Dissertations

The mitochondria are responsible for the bulk of energy production in eukaryotes. They possess their own genome that works in conjunction with the nuclear genome to accomplish the extraordinarily important task of energy conversion. When species hybridize there will be a mismatch in evolutionary histories between these two genomes. The deleterious interactions of these genomes have been studied in great detail (i.e. hybrid breakdown). However, little work has been conducted to understand the population genetic, and morphological consequences of wide-ranging replacement. The Fundulus notatus complex is comprised of 3 species: F. notatus, F. olivaceus, and F. euryzonus. Within the ...


Examination Of The Relevance Of Pi3k And Pten Pathway In Ustilago Maydis., Nathaniel Edward Dalton 2016 University of Louisville

Examination Of The Relevance Of Pi3k And Pten Pathway In Ustilago Maydis., Nathaniel Edward Dalton

Electronic Theses and Dissertations

Ustilago maydis is a fungal pathogen that is an obligate parasite on Zea mays (Corn) in order to undergo and complete its sexual life cycle. The cells grow as a haploid form until they meet a compatible partner and undergo a dimorphic switch from a budding yeast-like cell type to a filamentous dikaryon. Infection of the host plant is characterized by leaf chlorosis, anthocyanin content, and formation of large galls that develop on the stem, leaves, cobs, and flowers. Many signaling cascades such as MAPK and PKA are involved in the regulation of the infection lifecycle. The Phosphatidylinosotiol 3 Kinase ...


Molecular Measurement Of Toxicity In Fish; Case Examples And Policy Implications, Jessica A. Freedman 2016 University of Rhode Island

Molecular Measurement Of Toxicity In Fish; Case Examples And Policy Implications, Jessica A. Freedman

Senior Honors Projects

Stormwater and oil are common urban contaminants that can be harmful to fish species. One way of recognizing exposed and impaired fish is by monitoring gene expression and gene induction. This study focused on the identification and validation of reference genes for measuring contaminant-induced changes in gene expression due to urban influence. In this study, reference genes (which are genes used to normalize data and remain consistent in varying exposures regardless of organism and tissue type) were established. Six genes were identified as reference genes (ef1a, wdtc1, mtm1, spop, rxrba and tuba1) from a longer list of potential reference genes ...


American Chestnut Sem Portfolio, Dakota Matthews 2016 SUNY College of Environmental Science and Forestry

American Chestnut Sem Portfolio, Dakota Matthews

N.C. Brown Center for Ultrastructure Studies

Scanning electron microscopy micrographs of transgenic american chestnut pollen and anthers. Chinkapin anthers and pollen imaged also.


Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, Christopher J. Jones, David Newsom, Benjamin Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak 2016 The Ohio State University

Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, Christopher J. Jones, David Newsom, Benjamin Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak

Yasuhiko Irie

The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression ...


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