Molecular Characterization of the Transmission and Early Diversification of Hepatitis C Virus

Hepatitis C virus (HCV) is a medically important RNA virus in the Flaviviridae family. It persists in chronically infected individuals by replicating in hepatocytes and by evolving as a genetically diverse quasispecies that evades host immune pressures. However, transmission, with its attendant population bottlenecking, represents a period of relative vulnerability and is of particular importance with respect to viral natural history, immunopathogenesis, treatment intervention, and vaccine development. A precise molecular characterization of HCV transmission and early diversification has not previously been possible. In this dissertation work, it was hypothesized that HCV genomes that are transmitted from one individual to the next giving rise to productive clinical infection (termed transmitted/founder or T/F genomes) could be unambiguously identified by single genome sequencing (SGS), mathematical modeling, and phylogenetic inference. This hypothesis was tested in cohorts of acutely infected human subjects with community acquired HCV infection and in human-to-human and human-to-chimpanzee HCV transmission pairs. The resulting data showed that HCV transmission was generally associated with a stringent population bottleneck and that early virus evolution was characterized by diversification of discrete, low diversity sequence lineages. These findings enabled an unambiguous phylogenetic inference of T/F genomes, a precise characterization of early molecular pathways of viral sequence evolution, and a refined estimate of the in vivo mutation rate of HCV, which was at least 5-fold lower than previously reported. These efforts further allowed for the molecular identification, cloning, and analysis of full-length T/F viral genomes, which like most HCV clones, were restricted in their in vitro replication capacity. Altogether, our findings provide a substantially enhanced molecular view of HCV transmission and early diversification in natural human infection and illustrate a novel experimental approach to the proteome-wide analysis of HCV that may aid future vaccine development efforts

Larson forest restoration project historic range of variation (HRV reference conditions) assessment report. Special report to the Apache-Sitgreaves National Forests.

The Larson Forest Restoration Project (Larson Project) is located on the Apache-Sitgreaves National Forest (A-S N.F.), Black Mesa Ranger District. The project covers a landscape area of approximately 30,000 acres, dominated primarily by ponderosa pine (Pinus ponderosa), with some dry mixed conifer on the north facing slopes and an increase in alligator juniper (Juniperus deppeana) component on the dryer sites in the north portion of the project. The A-S N.F. asked the Ecological Restoration Institute (ERI) to help collect site-specific historical ecological data for the Larson Project area to establish site-specific reference conditions (forest conditions that were in place 130-140 years ago when frequent fire was still a dominant component of the ecological system). These reference conditions would be used by the interdisciplinary team (IDT) as a point of reference for forest restoration for project planning

Gerrymandering in Redlands, California

In April 2016, the City of Redlands, California, began the process of creating council electoral districts to comply with voting rights acts and avoid litigation. Several maps prepared by a consultant were being considered when, in May 2017, a group of graduate students from the University of Redlands produced this map. The Council agreed that this map was as good as or better than the consultant’s maps, but it was too late to consider a new map giving the legislative requirements. It will be considered after the 2018 elections

Fecal Bacteria Survival and Infiltration through a Shallow Agricultural Soil: Timing and Tillage Effects

Human and livestock exposure to fecal pathogens via contaminated surface or groundwater is an important water quality concern for soils receiving animal wastes. The effects of manure application timing (spring or fall application) and soil management (no-tillage or conservation tillage) on fecal bacteria infiltration through shallow karst soils in central Kentucky (the Bluegrass region) have not been evaluated. We performed a field experiment to measure fecal coliforms and fecal streptococci in leachate from dairy manure-amended no-tillage and conservation tillage soils. Manure significantly increased fecal bacteria in leachate compared with unmanured treatments. After manure application, the leachate that collected in zero-tension lysimeters 90 cm below the soil surface contained up to 6 × 104fecal coliforms/100 mL and generally exceeded 3 × 103 fecal coliforms/100 mL. Neither the timing nor the tillage method significantly affected fecal coliform concentrations in leachate. Fecal bacteria in leachate declined to nondetectable levels within 60 d of manure application. In the well structured soil used in this experiment, fecal bacteria moved below the crop root zone whenever there was rainfall of sufficient duration or intensity to cause flow after manure application. Manure application to no-tillage soil in spring did not accelerate water contamination by fecal coliforms relative to fall manure applications. No-tillage did not accelerate water contamination by fecal coliforms relative to tilled soils. The potential for groundwater contamination depended on soil structure and water flow more than on fecal bacteria survival at the soil surface

Fertilizer, Tillage, and Dairy Manure Contributions to Nitrate and Herbicide Leaching

Few studies have examined the water quality impact of manure use in no-tillage systems. A lysimeter study in continuous corn (Zea mays L.) was performed on Maury silt loam (fine, mixed, semiactive, mesic Typic Paleudalf) to evaluate the effect(s) of tillage (no-till [NT] and chisel-disk [CD]), nitrogen fertilizer rate (0 and 168 kg N ha−1), and dairy manure application timing (none, spring, fall, or fall plus spring) on NO3–N, atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine), and alachlor [2-chloro-2′-6′-diethyl-N-(methoxymethyl)acetanilide] concentrations in leachate collected at a 90-cm depth. Herbicides were highest immediately after application, declining to less than 4 μg L−1 in about two months. Manure and manure timing by tillage interactions had little effect on leachate herbicides; rather, the data suggest that macropores rapidly transmitted atrazine and alachlor through the soil. Tillage usually did not significantly affect leachate NO3–N, but no-tillage tended to cause higher NO3–N. Manuring caused higher NO3–N concentrations; spring manuring had more impact than fall, but fall manure contained about 78% of the N found in spring manure. Nitrate under spring “only fertilizer” treatment exceeded 10 mg L−138% of the time, compared with 15% for spring only manure treatment. After three years, manured soil leachate NO3–N exceeded that for soil receiving only N fertilizer. Soil profile (90 cm) NO3–N after corn harvest exceeding 22 kg N ha−1 was associated with winter leachate NO3–N greater than 10 mg N L−1 Manure can be used effectively in conservation tillage systems on this and similar soils. Accounting for all N inputs, including previous manure applications, will be important

Infiltration of Fecal Bacteria Through Soils: Timing and Tillage Effects

Land-applying animal wastes potentially exposes humans and animals to fecal pathogens, either by direct contact with soil and produce, or via ground water contamination. Some of these organisms are Salmonella, certain pathogenic Escherichia coli strains, protozoa such as Cryptosporidium and Giardia, and enteric viruses. Whether soil adequately filters these pathogens before they reach ground water depends on the interaction of porosity, texture, depth, water content, rainfall intensity and duration, and soil management

Fertilizer, Tillage, and Dairy Manure Contributions to Nitrate and Herbicide Leaching

Few studies have examined the water quality impact of manure use in no-tillage systems. A lysimeter study in continuous corn (Zea mays L.) was performed on Maury silt loam (fine, mixed, semiactive, mesic Typic Paleudalf) to evaluate the effect(s) of tillage (no-till [NT] and chisel-disk [CD]), nitrogen fertilizer rate (0 and 168 kg N ha−1), and dairy manure application timing (none, spring, fall, or fall plus spring) on NO3–N, atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine), and alachlor [2-chloro-2′-6′-diethyl-N-(methoxymethyl)acetanilide] concentrations in leachate collected at a 90-cm depth. Herbicides were highest immediately after application, declining to less than 4 μg L−1 in about two months. Manure and manure timing by tillage interactions had little effect on leachate herbicides; rather, the data suggest that macropores rapidly transmitted atrazine and alachlor through the soil. Tillage usually did not significantly affect leachate NO3–N, but no-tillage tended to cause higher NO3–N. Manuring caused higher NO3–N concentrations; spring manuring had more impact than fall, but fall manure contained about 78% of the N found in spring manure. Nitrate under spring “only fertilizer” treatment exceeded 10 mg L−138% of the time, compared with 15% for spring only manure treatment. After three years, manured soil leachate NO3–N exceeded that for soil receiving only N fertilizer. Soil profile (90 cm) NO3–N after corn harvest exceeding 22 kg N ha−1 was associated with winter leachate NO3–N greater than 10 mg N L−1 Manure can be used effectively in conservation tillage systems on this and similar soils. Accounting for all N inputs, including previous manure applications, will be important

Native plants dominate understory vegetation following ponderosa pine forest restoration treatments

Dense ponderosa pine forests in the southwestern United States inhibit understory production and diversity and are susceptible to high-severity wildfire. Restoration treatments involving overstory thinning and prescribed burning are being implemented to increase understory productivity and diversity and to reduce the risk of severe wildfire. However, disturbances associated with treatments may favor invasion of nonnative species, and the severity of the disturbance may be related to the level of nonnative species establishment. We examined understory community composition, species richness, and plant cover responses to 3 stand-scale replicates of 4 different tree-thinning intensities. Restoration treatments altered the composition of the understory community regardless of thinning intensity. Understory richness and cover were highly variable among experimental blocks, but we observed strong trends of increasing richness and cover in the treated stands. Immediately following restoration treatments, nonnative species cover comprised 6% of the total cover where treatment-induced disturbances were the greatest. However, the initial increase in nonnative species did not persist and was reduced by half 6 years after treatment. Plant community composition was still in flux by the sixth year after treatment, indicating that continued monitoring is necessary for evaluating whether restoration targets are maintained over time