MicroRNAs (miRNA) are a type of non-coding small RNA (smRNA) that regulate gene expression at the post-transcriptional level by base pairing with complementary sites in messenger RNA (mRNA), causing either mRNA degradation or translational inhibition. The overall goal of this project is to understand the relationship between miRNAs and abiotic stresses in plants. How plants employ miRNAs to alter gene expression when they encounter various stresses, like drought, cold, submergence, and salinity, is of great agricultural importance. Plants must develop sophisticated ways to cope with these stresses since they are unable to evade them. We first utilized small RNA biogenesis mutants such as dcl1, dcl2/3/4, or rdr2 to enrich specific small RNAs, and then used these mutants to make smRNA libraries. We treated Arabidopsis rdr2 seedlings with submergence, salt, and both submergence and salt, while treating Arabidopsis rdr2 flowers with drought, salt, and cold. Their low molecular weight RNA were isolated, and smRNA libraries were constructed. We checked the quality of the libraries by traditional cloning and sequencing. From these smRNA libraries, miRNA expression will be analyzed by high-throughput sequencing by SBS (sequencing by synthesis) and sent to a company (Illumina) or a facility at the Delaware Biotechnology Institute to sequence, and then for data mining by computational analysis. Potential miRNA candidates will be identified and undergo validation. R.S.H.B was supported by Delaware EPSCoR, through National Science Foundation Grant EPS-0447610 and the State of Delaware, and NSF grant MCB#0548569 to P.J.G. provided research support.

White rot fungi, specifically Phanerochaete chrysoporium, are able to produce non-stereo selective enzymes that oxidize compounds present in pollutants and, therefore, may be used for environmental remediation. Past research has investigated the ability of the fungal enzymes, lignin peroxidases (LiP) and manganese-dependent peroxidases (MnP), to degrade pesticides and other compounds present in wastewater and the herbicides, atrazine and alachlor, in contaminated soil. Although past studies have successfully measured the percentage of compound degradation, there still remain difficulties with measuring the enzyme activity after application to the soil due to interacting compounds. The goal of this research is to develop an assay and method to monitor the activity of LiP and MnP within the soil over time. The fungi have been grown within a packed-bed bioreactor, first supplied with growth media and then starvation media which cause the fungi to begin the ligninolytic activity. Once the fungi begin producing enzymes, the effluent will be collected and applied to soil. The enzymes will be extracted from the soil using the developed assay. The soil extract will be analyzed for enzyme activity. LiP activity will be monitored by using a continuous spectrophotometric assay that measures the oxidation of veratryl alcohol to veratraldehyde at 310 nm. MnP activity will be monitored by using a continuous spectrophotometric assay to measure the oxidation of o-dianisidine to a colored-product at 460 nm.  Future work will evaluate the efficiency of this proposed method and continue examining literature for other enzyme extraction methods from soil. Research funded by Delaware EPSCoR, through National Science Foundation Grant EPS-0447610 and the State of Delaware.

The chicken was domesticated approximately 7,000-10,000 years ago in Asia from the red jungle fowl. The advent of industrial scale agriculture in the early 20th century triggered intensive genetic selection to improve the chicken’s meat (broiler) production traits. This selection has yielded birds with a 2 fold increase in breast muscle mass and a significantly reduced time to market. Along with increased muscle, undesirable traits have arisen including cardiovascular failure leading to sudden death. We are comparing a heritage line (IL50) that grows as broilers did in the 1950s with a modern line (Ross708) to gain insight into the changes resulting from the selective pressure. A morphometric analysis revealed significant growth differences between the heart, breast muscle and liver of the heritage and modern lines. Current effort focuses on determining the size and number of cells in the heart and breast muscle of the two lines. This will allow evaluation of the relative contributions of hypertrophy and hyperplasia to the overall size of the organs. This research was funded by INBRE.

Increasing areas of residential development combined with the loss of forested land is an environmental concern in Delaware. There has been a 35% increase in urban land use throughout Delaware from 1992 to 2002. These land use changes throughout the state can contribute to impaired water quality issues. Proper land use balance is essential in order to protect the health of nearby bodies of water. The objective of this research was to determine the effect of current and potential future land use changes on the fate and transport of runoff, sediment erosion, and nitrate-nitrogen and phosphate-phosphorus deposition within the Mispillion watershed using the Loading Simulation Program C++ (LSPC). Land use type was altered for the Mispillion watershed to represent a present day calibration simulation (2001-2003), a future residential build-up, and a historic pre-colonial era where forest was the dominant land use. Results indicate that the large presence of agricultural land within the watershed combined with rainfall events are the defining factors for the output values of runoff, sediment loss, and nutrient deposition. These findings as well as the continued use of the LSPC model can provide land use planners quantitative information that is essential for making sound environmental decisions. Future simulation analyses will include growth projection estimates for the Mispillion watershed from the Delaware State Office of Planning. This project described was supported by Delaware EPSCoR, through National Science Foundation Grant EPS-0447610 and the State of Delaware.

Salmonella is one of the major causes of food borne illness, and serovars Typhimurium and Enteritidis among the more commonly isolated serovars from the infected humans. Serovar Kentucky is only rarely found in humans, but is the most prevalent serovar in chickens in the United States. This serovar appears to be more sensitive to low pH induced by hydrochloric acid, which could be one of the reasons for its low infectivity in humans. The purpose of this study was to compare gene expression under hydrochloric acid-induced conditions of a S. enterica Kentucky and Enteritidis serovar. The two isolates were grown in rich medium of pH 8 until mid-logarithmic phase, then the pH of the growth medium was lowered to 4.5 by addition of 10 N HCl. Total RNA was isolated from the bacteria after a 10-min exposure to the acid conditions using RNase Protect and the Qiagen RNeasy® Mini Kit. The RNA was dried under vacuum and sent to the USDA Agricultural Research Service in Georgia for microarray hybridization The microarray data showed a very similar gene expression profile in the two serovars, but some operons were upregulated in the Kentucky isolate, but not in the Enterititdis isolate. These operons included the pdu (propanediol-utilization) genes, the cbi (vitamin B12 synthesis) genes, putative hydrogenase gene STM1538 and asrABC (encoding anaerobic sulfite reduction genes). The significance of these findings is currently unknown and further gene expression studies will have to be carried out to elucidate differences in acid response between Salmonella serovars.

The suburban sprawl in the northeastern states has created refuge areas for white-tailed deer (Odocoileus virginianus) populations to drastically increase. These refuges prevent deer population control by limiting hunting access because of mandated safety zones. The balance between public safety and deer population control is a challenge for wildlife managers. Northern Delaware is a prime example of a densely human populated area with a large deer population. We examined possible impacts of altering safety zone size on the amount of land accessible to hunting. Using an aerial photograph of New Castle County, Delaware north of I-95 and I-495, a 183m (200yrds) buffer was established around each inhabited building, which represents the size of the current safety zone. Using this buffer we were able to quantify the current land available for hunting. We altered the buffer size around each building from 183m (200yrds) to 91m (100yrds) and 46m (50yrds) to determine the total area of deer habitat accessible for harvest under smaller safety zone sizes. By analyzing this data it was established that by reducing the safety zone to a reasonable 91m (100yrds), 71% of the land considered deer habitat would be available for harvest. By reducing the safety zone distance wildlife managers could have a more effective tool for controlling deer population and thus deer tick related diseases and environmental damages due to deer browsing. This study was supported by Delaware EPSCoR, through National Science Foundation Grant EPS-0447610 and the State of Delaware

In the poultry industry, table egg laying hens are used to produce the eggs that are bought in the grocery store. Multiple layers are kept in one cage with 10,000 to 18,000 cages and 75,000-125,000 or more birds in a typical layer house.  In the poultry industry, the primary approach to highly infectious diseases is surveillance, quarantine, depopulation, disposal, and disinfection.  When birds are infected or suspected of infection, with a highly infectious disease, such as avian influenza, the birds must be depopulated in order to prevent the spread of the disease.  Depopulation methods have been developed for floor reared meat type birds, but caged layers remain a problem.  One of the critical questions is whether to depopulate the birds inside the cages or to remove the birds prior to depopulation.  After death, during rigor mortis, it becomes difficult to remove the birds from the cages. The purpose of this experiment was to determine the average rigor mortis onset and relaxation time for depopulated caged layer carcasses.  This will help determine when are the most efficient times for removing the carcasses from the cages, so that disposal of the carcasses and disinfection of the facilities can begin. This study was supported by Delaware EPSCoR, through National Science Foundation Grant EPS-0447610.