To What Extent Does DNA Methylation Affect Phenotypic Variation in Cattle?

DNA methylation is an environmentally influenced epigenetic modification that regulates gene transcription and has the potential to influence variation in economically important phenotypes in agricultural species. We have utilized a novel approach to evaluate the relationship between genetic and epigenetic variation and downstream phenotypes. To begin with, we have integrated RNA-Seq and methyl binding domain sequencing (MBD-Seq) data in order to determine the extent to which DNA methylation affects phenotypic variation in economically important traits of cattle. MBD-Seq is a technique that involves the sample enrichment of methylated genomic regions followed by their next-generation sequencing. This study utilized Illumina next generation sequencing technology to perform both RNA-Seq and MBD-Seq. NextGENe software (SoftGenetics, State College, PA) was employed for quality trimming and aligning the sequence reads to the UMD3.1 bovine reference genome, generating counts of matched reads and methylated peak identification. Subsequently, we identified and quantified genome-wide methylated regions and characterized the extent of differential methylation and differential expression between two groups of animals with extreme phenotypes. The program edgeR from the R software package (version 3.0.1) was employed for identifying differentially methylated regions and regions of differential expression. Finally, Partial Correlation with Information Theory (PCIT) was performed to identify transcripts and methylation events that exhibit differential hubbing. A differential hub is defined as a gene network hub that is more highly connected in one treatment group than the other. This analysis produced every possible pair-wise interaction that subsequently enabled us to look at network interactions of how methylation affects expression. (co-expression, co-methylation, methylation x expression). Genomic regions of interest derived from this analysis were then aligned to previously identified QTL and GWAS regions using Animal QTL database. The approach described here has provided us with evidence that QTL and GWAS regions overlay genomic regions where methylation may regulate transcription

Characterisation of trimethoprim resistance transposons and their gene products

A faecal enterobacterial strain, P-20, isolated from pigs, was shown to owe its trimethoprim resistance to two different plasmid/transposon mediated resistance genes. One gene, mobilised by RP4, was located on a 4 - 6 kb transposon designated Tn4135, and resulted in the mediation of transferable high level trimethoprim resistance of greater than 1000 ug/ml. Biochemical investigation of the transposon gene product revealed a close resemblence between the trimethoprim resistant dihydrofolate reductase (DHFR) of Escherichia coli J62(RP4::Tn4135) and that of the type I plasmid enzyme, encoded by RP4::Tn7_. Despite the differences in transposon size, this marked similarity between the two DHFRs suggests a similar evolutionary origin for the two transposons and reiterates the potential of trimethoprim resistance transfer between animal and human resevoirsDetailed biochemical and genetic studies indicated that the second trimethoprim resistance gene of the pig isolate, P-20, mobilised by Sa-1 (Sa-1::Tn4135ORI), bore very little similarity with any previously isolated DHFR. The specific activity of the enzyme was 10 fold lower than that of the type I-like enzyme encoded by RP4::Tn4135, and this, coupled with differences in enzymic properties and the failure to hybridize with type I or type II gene probes, suggests the presence of a new enzyme - a type VI - of distinct evolutionary origin.The incompatibility group W plasmid, Sa, was investigated for its role as a stable recipient for amplifiication studies of Tn4135, but molecular weight determination, resistance testing and restriction enzyme analysis revealed that this plasmid was not as stable as expected. This plasmid appeared in two forms, Sa-1 and Sa-2; the former being 15 kb smaller, which resulted from a deletion of DNA encoding the chloramphenicol resistance gene. This instability was further reflected in the size variations of Sa plasmid DNA harbouring trimethoprim resistance transposons. Examination of transconjugants from the transfer of Tn4135 from RP4 to Sa-1, in contrast with transfer to Sa-2, indicated that this transposon could transfer in an aberrant fashion, resulting in the formation of an enlarged plasmid species (Sa-1::Tn4135a). The mechanism(s) behind the generation of such a large species were obscure, but appear to involve a combination of multiple transposition, gene amplification, replicon fusion and transposon-mediated transfer of plasmid DNA. Examination of Tn7 transposition to Sa-2 indicated that this transposon was also capable of generating aberrant forms, and reiterated the similarity between the RP4::Tn7_ and RP4::Tn4135 encoded genes

The personal and contextual factors influencing teacher agency and self-efficacy when planning and implementing individual education plans : a thesis presented in partial fulfilment of the requirements for the degree of Master of Educational Psychology at Massey University, Palmerston North, Manawatū, New Zealand

There is an increasing amount of literature that examines how teacher agency and self-efficacy influence inclusive education. Research demonstrates that when teachers feel confident in their capabilities, they are capable of actions that allow them to teach in a more inclusive manner. Individual Education Plans (IEPs) are one tool teachers can collaboratively use to support students with disabilities to access the curriculum. This study explores the personal and contextual factors that influence teacher agency and self-efficacy when planning and implementing IEPs by using a mixed-methods explanatory-sequential design. Participants were 42 primary school teachers without positions of senior responsibility, from the North Island of New Zealand. Each teacher had participated in at least one IEP in the last twelve months. Phase one employed an e-questionnaire, followed by four semi-structured interviews in phase two. The e-questionnaire measured participant’s perceived self-efficacy, and examined their perceptions of the IEP process, and experiences of professional learning and development (PLD) related to the planning and implementation of IEPs. Face-to-face interviews explored and expanded on phase one themes. Results demonstrated that a number of personal and contextual factors influence teacher agency when planning and implementing IEPs. Strong pedagogical knowledge, teaching experience, the ability to form collaborative relationships, and understanding the teacher’s role in an IEP team were required for teachers to experience enhanced self-efficacy and agency. Having collaborative relationships within the IEP team, time, and inclusive school policies were contextual factors that enabled and inhibited teacher agency and self-efficacy. While the majority of participants had not received PLD relating to planning and implementing IEPs, they identified that efficacious PLD would need to be specific and needs-based, collaborative in approach, expert facilitated and readily available to enhance teacher self-efficacy and enable agency when planning and implementing IEPs. Primary teachers in New Zealand would benefit from school management providing teachers with increased PLD on the use of IEPs and inclusive education, if they are to experience high self-efficacy and achieve agency when planning and implementing IEPs for students with disabilities

Bridging The CPA Exam Gap: Do Internships Matter?

In this paper we consider whether experience gained on the job through an internship results in knowledge that can help with passing the CPA exam. It would seem that a candidate for the CPA exam would be better prepared if they had the combination of education and practical experience. We examine the CPA exam performance of 72 graduate students that completed a public accounting internship prior to sitting for the CPA exam compared to 98 graduate students that did not complete an internship in public accounting. Our analysis indicates that on average students completing internships score higher on all parts of the CPA exam. In addition, on average, students completing internships had a higher overall pass rate for each section of the exam, with the pass rate for the Regulation (REG) section being significantly higher for students that have completed internships; we also find that on average students with internships pass 2 sections of the exam prior to graduation as compared to 1.69 for students that have not completed internships

Searching for Hyperspectral Optical Proxies to Aid Chesapeake Bay Resource Managers in the Detection of Poor Water Quality

Shellfish aquaculture is a growing industry in the Chesapeake Bay. As population grows near the coast, extreme weather events cause a greater volume of pollutant runoff from impervious surfaces and agricultural lands. Resource managers who monitor shellfish beds need reliable information on a variety of water quality indicators at higher frequency than is possible through field monitoring programs and at a higher level of detail than current satellite products can provide. Although many factors causing degraded water quality that can impact human health are not currently discernable by traditional multispectral techniques, hyperspectral imagery offers a new opportunity to detect phytoplankton communities associated with harmful algal blooms and biotoxin production. Together with resource managers in their routine monitoring of sites around the bay from small boats, we have been exploring remotely sensed optical proxies for the detection of harmful algal blooms and sewage. Early warning by remote sensing could guide sampling and improve the efficiency of shellfish bed closures, ultimately improving health outcomes for humans and animals. An extensive network of routine sampling by Chesapeake Bay Program managers makes this is an ideal location to develop and test future satellite data products to support management decisions. Next generation hyperspectral measurements from the future Plankton Aerosol Cloud ocean Ecosystem (PACE) mission at nearly daily frequency, combined with the potential of higher spatial resolution from the Surface Biology and Geology (SBG) observing system recommended in the recent Decadal Survey, along with high frequency observations from the newly selected Geostationary Littoral Imaging and Monitoring Radiometer (GLIMR) Earth Venture Instrument make this a critical time for defining the needs of the aquaculture and resource management community to save lives, time, and money

Cultivating Institutional Capacities for Learning Analytics

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138371/1/he20243.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138371/2/he20243_am.pd

Mass Murderers: A Case Study Analysis of Social Media Influence and Copycat Suicide

The frequency of mass murder has increased over the past decade, with nearly half of all mass murderers committing suicide. Previous researchers have found imitations of mass murderers which relate to suicide contagion, media contagion, and copycat effects; however, there remains a gap in the literature pertaining to the connection between copycat suicides of mass killers and the influence of social media. The purpose of this study was to provide a greater understanding of U.S. public mass murderers who commit copycat suicides based on the influence of social media. The constructivist conceptual framework guided the examination of a purposeful sample of 12 American mass murderers who committed suicide. The research questions aligned with Murray’s transcendent fantasy theory and Bandura’s social learning theory, and included an analysis of publicly available data. Six themes were identified among public mass murderers in the United States who committed suicide: (a) preoccupation with previous mass murderers, (b) suicidal ideation (suicidal thoughts and planning and prior suicide attempts), (c) extreme isolation and computer use (social media, Internet, and violent video games), (d) presence of copycat behavior, (e) fame-seeking fantasies and media attention, and (f) preoccupation with the Columbine shooters. These findings contribute to existing research about mass murder, copycat behaviors, and social media influence. Bringing greater awareness of mass murderers, copycat suicides, and social media influence to the public, law enforcement, media outlets, and other stakeholders will promote improved identification and intervention of potential mass killers, as well as the educated distribution of information related to mass murder via social media, so that improved actions and reactions occur in society, enhancing positive social change

Surficial Geology of the Burr Oak (Iowa) 7.5\u27\u27 Quadrangle,

https://ir.uiowa.edu/igs_ofm/1049/thumbnail.jp

Bedrock Geology of the Shell Rock 7.5\u27 Quadrangle, Butler, Black Hawk and Bremer counties, Iowa

https://ir.uiowa.edu/igs_ofm/1062/thumbnail.jp