DRUM Community: College of Agriculture & Natural Resources

Assessing the uncertainty of emergy analyses with Monte Carlo simulations

Sun, 01 Jan 2012 00:00:00 GMT

Title: Assessing the uncertainty of emergy analyses with Monte Carlo simulations Authors: Hudson, Amy Abstract: Crop production systems were used to show the presence and propagation of uncertainty in emergy analyses and the effect of source variance on the variance of the yield unit emergy value (UEV). Data on energy/masses and UEVs for each source and yield were collected from the emergy literature and considered as inputs for the Monte Carlo simulation. The inputs were assumed to follow normal, lognormal, or uniform probability distributions. Using these inputs and a tabular method, two models ran Monte Carlo simulations to generate yield UEVs. Supplemental excel files elucidate the Monte Carlo simulations' calculations. The nitrogen fertilizer UEV and net topsoil loss energy were the inputs with the largest impact on the variance of the yield's UEV. These two sources also make the largest emergy contributions to the yield and should be the focus of a manager intent on reducing total system uncertainty. The selection of a statistical distribution had an impact on the yield UEV and thus these analyses may need to remain system- or even source- specific.

GENOME-WIDE ANALYSIS OF CHICKEN MIRNAS AND DNA METHYLATION AND THEIR ROLES IN MAREK'S DISEASE RESISTANCE AND SUSCEPTIBILITY

Sun, 01 Jan 2012 00:00:00 GMT

Title: GENOME-WIDE ANALYSIS OF CHICKEN MIRNAS AND DNA METHYLATION AND THEIR ROLES IN MAREK'S DISEASE RESISTANCE AND SUSCEPTIBILITY Authors: Tian, Fei Abstract: Marek's disease (MD) is a T cell lymphoma in chickens and causes high mortality and morbidity in productive chickens. Two inbred chicken lines, resistant line 63 and susceptible line 72, with the same MHC haplotype, showed distinct disease outcomes after MDV infection. The current studies aimed to illustrate the role of microRNA (miRNAs) and DNA methylation in MD resistance and susceptibility in chickens. First, to ascertain the function of miRNAs, miRNA microarray experiments were used to identify miRNAs sensitive to MDV infection in the 2 lines. Most miRNAs were repressed in line 72 after MDV infection, while their transcription was steady in line 63. The miRNA target genes were identified in chickens. Cellular miRNA gga-miR-15b and gga-let-7iwere reduced in infected line 72 chickens and MD tumors. The downregulation of the two miRNAs increased the expression of ATF2 (activating transcription factor 2) and DNMT3a (DNA methyltransferase 3a) in infected line 72. These results indicated that miRNAs may play antiviral functions through modulating target gene expression. Next, to characterize the role of miRNAs in MDV infection, the selected chicken miRNAs were overexpressed in MDV infected DF-1 cells. The overexpressions of chicken miRNA gga-miR-15b and gga-let-7i, by using the retroviral based vector, significantly restricted MDV replications in vitro. MDV oncoprotein was repressed, suggesting that chicken miRNAs may limit MDV propagation. Finally, we found deregulation of transcription of DNA methyltransfereases (DNMTs) in lines 63 and 72 after MDV infection, which coordinated with the methylation alterations in the 2 lines. Infection induced differential methylation regions (iDMRs) that were identified through genome-wide DNA methylation quantification. Genes overlapping line-specific iDMRs were related with pathways of different functions in these two lines, implying the involvement of DNA methylation in MD- resistance and susceptibility. An in vitro study showed that DNA methylation inhibitor repressed viral spread and viral replication. In conclusion, the observed variations of miRNA expression and DNA methylation may be associated with disease predisposition in chickens.

TRANSMISSION OF CYMBIDIUM MOSAIC VIRUS IN ONCIDIUM ORCHIDS BY PERIPLANETA AUSTRALASIAE

Sun, 01 Jan 2012 00:00:00 GMT

Title: TRANSMISSION OF CYMBIDIUM MOSAIC VIRUS IN ONCIDIUM ORCHIDS BY PERIPLANETA AUSTRALASIAE Authors: Allen, Carol Dianne Abstract: ABSTRACT Title of Thesis: TRANSMISSION OF CYMBIDIUM MOSAIC VIRUS IN ONCIDIUM ORCHIDS BY PERIPLANETA AUSTRALASIAE Carol Dianne Allen, Master of Science. 2012 Thesis Directed by: Gary Coleman, Ph.D. Department of Plant Science and Landscape Architecture Cymbidium mosaic virus is the most common disease in orchids infecting a large number of cultivated orchids found in all phases of the industry and around the world. Its transmission occurs through contact by contaminated cutting tools, human hands, or water. Although insects known to transmit plant viruses have been exposed to orchid viruses, none have been found to successfully transmit Cymbidium mosaic virus. Periplaneta australasiae, the Australian cockroach, is a common greenhouse pest that is known to feed on orchid plants. In controlled conditions Australian cockroaches were given inoculation access through feeding activity on known CymMV positive orchid plants and then allowed to feed on virus free plants. The virus free plants were isolated from subsequent insect exposure and after a period of time samples from the feeding damage sites were analyzed for the presence of virus RNA through nested and hemi-nested PCR techniques. A statistically significant number of samples were positive demonstrating that with high population numbers and long term exposure, virus transmission is possible.

Review of the Molecular Biology and Epidemiology of Infectious Laryngotracheitis (Gallid Herpesvirus-1)

Sun, 01 Jan 2012 00:00:00 GMT

Title: Review of the Molecular Biology and Epidemiology of Infectious Laryngotracheitis (Gallid Herpesvirus-1) Authors: Menendez, Kimberly Rae Abstract: A review of the molecular biology and epidemiology of avian infectious laryngotracheitis (ILT) is conducted due to the outdated state of current ILT review material. The objective of this review is to include updated information on the molecular biology of Gallid herpesvirus 1 (GaHV-1), the causative agent of ILT, and to present the latest information on the molecular epidemiology of ILT. Recent developments in molecular biology specific to GaHV-1 have been made and are highlighted in this review, and the role of current and historical use of live-attenuated vaccines is associated with the global and molecular epidemiology of ILT. Also, target genes for detection and strain differentiation are compiled by region of the world, and the global distribution of ILT is illustrated. Additionally, the field of epigenetics related to virus-host interactions is reviewed, and the molecular, epidemiologic, and epigenetic factors investigated are related to prospects for future eradication of ILT.