Evaluating the impacts of Midwestern cropping systems on soil health and subsurface drainage water quality

Agricultural nutrient management practices are an important component of the effort to improve water quality in the Mississippi River Basin. In particular, there is concern about nutrient export to the Gulf of Mexico via loss from subsurface drainage systems. Optimizing the use of fertilizers and animal manures in combination with other management practices has the potential to minimize negative impacts on water quality. Farmers are increasingly challenged to maximize crop production while utilizing fertilizers and animal manures in an efficient and environmentally friendly manner. An increasing awareness of the potential to address these issues by improving soil health has also led to significant interest in quantifying the impact of cropping management practices on soil health indicators. The objectives of the first study in this thesis were to investigate the effects of crop rotation, tillage, corn residue removal, swine manure, and cereal rye (Secale cereale) cover crops on nitrate-N (NO3-N) and dissolved P (PO4-P) losses via subsurface drainage. The study was evaluated from 2008 through 2015 using thirty-six 0.4 ha plots outfitted with a subsurface drainage water quality monitoring system. Results showed that swine manure applied prior to both corn (Zea mays L.) and soybean (Glycine max (L.) Merr.) had significantly higher flow-weighted NO3-N concentrations compared to swine manure applied before corn only. Total NO3-N losses from the treatments ranged from 15.2 to 29.5 kg N ha-1 yr-1. The cereal rye cover crops reduced NO3-N loss, whereas tillage and residue management had little impact. The treatments had minimal impact on PO4-P leaching. Total PO4-P losses averaged \u3c 32 g P ha-1 yr-1 from all treatments, which was very low in comparison to some drainage studies in the upper Midwest. The objectives of the second study were to evaluate the effects of liquid swine manure application timing, crop rotation, cereal rye cover crops, and a nitrification inhibitor on drainage water quality and grain yields. The study was evaluated in 2016 and 2017 on the same plots as the first study. Results showed that early fall applied swine manure (EFM) with a rye cover crop resulted in significantly lower 2-yr average NO3-N concentrations and losses compared to EFM without a cover crop in a corn–soybean (CS) rotation. Spring application of urea ammonium nitrate (UAN) had significantly lower 2-yr average N losses compared to treatments receiving EFM or LFM in CS rotations. Average rye N uptake was significantly greater in plots receiving EFM application prior to corn (88 kg N ha-1) compared with plots receiving no manure prior to soybeans (51 kg N ha-1). There were no significant differences in 2-yr average NO3-N concentrations or losses in continuous corn (CC) treatments receiving either LFM or spring manure (SM). Yields in CC were significantly higher with SM compared to LFM. In CS rotations, 2-yr average corn yields were greatest with spring-applied UAN \u3e LFM without cover crop \u3e EFM without cover crop = EFM with cover crop. Soybean yields were lowest in the EFM with cover crop treatment. Delaying manure application until late fall rather than early fall, or spring rather than late fall, resulted in an economic advantage due to higher corn yields. The results indicate that the rye cover crop was effective for improving water quality and capturing N from manure. The third study investigated the long term effects of tillage, corn residue removal, liquid swine manure applications, and cereal rye cover crops on soil health indicators. Total soil carbon (TC) levels were monitored annually to a depth of 120 cm over a 10-yr period from 2007 to 2016. In the spring of 2017, soil cores were taken to a depth of 15 cm and analyzed for TC, aggregate size distribution, bulk density, potentially mineralizable nitrogen, pH, P, and K levels. This data was evaluated with the Soil Management Assessment Framework to quantify an overall soil quality index (SQI) score in five different treatments. Results show that from 2007 to 2016, TC levels remained unchanged to a depth of 30 cm but increased in all treatments at a depth of 60 to 90 cm. There were also increases at the 30 to 60 cm and 90 to 120 cm depths in some treatments. The rate of change in TC at a given depth did not differ between treatments. In the 2017 soil cores, aggregate size distribution differed between treatments but there was no significant difference in the overall fraction of aggregates \u3e 212 ïÿým. Bulk density levels were significantly higher in no-till compared to treatments with tillage. Potentially mineralizable nitrogen levels did not differ significantly between treatments. Overall SQI scores in the five treatments differed significantly, with CC treatments having the highest SQI score and a no-till + cover crop treatment having the lowest SQI due to higher bulk density and lower TC than other treatments

Removal Of Perchlorate From Drinking Water And Ion-Exchange Regenerant Brines

Perchlorate ions from rocket fuel, flare and munitions manufacture and use have escaped into groundwater in several states in the USA. Perchlorate causes alarm because it mimics iodine physiologically and is adsorbed by the thyroid gland, subsequently interfering with the endocrine systems of the brain. Removal of perchlorate to very low ppb is difficult on two fronts: competing ions such as nitrate, sulfate, carbonate etc. are often present at 1000 times higher concentration than perchlorate, and perchlorate is surprisingly stable considering its reputation as a rocket fuel oxidant. Direct electrochemical reduction of perchlorate in the parts per billion range is too slow and expensive to be viable. Ion exchange produces a troublesome disposal problem: either a perchlorate laden ion exchange resin or a brine stream containing high concentrations of perchlorate, nitrate, sulfate and bicarbonate. Electrochemical redox reduction of perchlorate, coupled to ion exchange capture and concentration is an economic and elegant method of dealing with both nitrate and perchlorate, particularly if the kinetics of the reduction process are fast. Perchlorate is surprisingly stable to reduction at a reducing cathode and with common reducing redox ions such as Cr2+, Fe2+. The reaction of perchlorate with Ti3+ is well documented in the literature, but the kinetics are slow in common solutions. In our latest study we have discovered that the reaction of perchlorate with titanium ions in methanesulfonic acid is very fast. We describe the laboratory experiments and pilot plant field trials in California that demonstrate the utility of this method for removing perchlorate and nitrate directly from drinking water and from regenerant brines from ion exchange systems

Harvest and Storage of Weather-damaged Corn for Silage

Extreme weather events may lead to a decision to make corn silage rather than harvest corn for grain, or to harvest acres that will exceed current silage storage capacity. Before harvesting for silage, make sure you have a market for the silage or a sufficient number of livestock to feed it to. It may be difficult to harvest good quality corn silage if the crop has weather damage and the economic value of the silage will likely be lower than silage from non-damaged fields. The resources section has links to information that can help with pricing forages in the field and determining the economic value of corn silage

Biochar as a cover for dairy manure lagoons: reducing odor and gas emissions while capturing nutrients

Liquid manure lagoons are known to be sources of odor and environmentally damaging gas emissions. Land application of the manure slurry after storage can lead to detrimental nutrient runoff and leaching. Floating lagoon covers (biocovers) are one option for reducing emissions, but to date they have only been used to address odors and emissions but not to address the problem of nutrient loss. This study evaluated the potential of floating biochar covers to reduce odor and gas emissions while simultaneously capturing nutrients from liquid dairy manure. The unique physical and chemical properties of biochars make them promising materials for odor, gas, and nutrient sorption. This new approach has the potential to mitigate multiple environmental problems. Two biochars were used to test this approach: one made from Douglas-fir chips under a low oxygen combustion environment at 650°C (FC650), and the other made from Douglas-fir hog fuel pyrolyzed at 600°C (HF600). The HF600 biocover reduced mean headspace ammonia (NH₃) concentration by 7.5 to 13.6 μL/L. No significant reduction was found with the FC650 biocover. These biochars were able to sorb and hold nutrients while floating on the surface. Nutrient uptake by the two biochars ranged from 0.21 to 4.88 mg nitrogen g biochar⁻¹ and 0.64 to 2.70 mg phosphorus g biochar⁻¹. Potassium ranged from a loss of 4.52 to a gain of 2.65 mg g biochar⁻¹. The biochars also sorbed calcium, magnesium, sodium, iron, aluminum, manganese, and silicon. In a separate experiment, a panel of judges evaluated the odor offensiveness (-10 to 10 scale) and odor threshold (1 to 10 scale) of five cover treatments including four biochars. Mean odor offensiveness ranged from -0.4 to -1.4 vs. -2.1 for the control. Mean odor threshold ranged from 1.6 to 2.1 vs. 2.6 for the control. These results show that biochar covers hold promise as an effective means for reducing odor and gas emissions while sorbing nutrients from liquid dairy manure. More research is needed to determine optimal biochar feedstock, production temperature, pH, and particle size distribution for use as a biocover material

Reverse genetics through random mutagenesis in Histoplasma capsulatum

<p>Abstract</p> <p>Background</p> <p>The dimorphic fungal pathogen <it>Histoplasma capsulatum </it>causes respiratory and systemic disease in humans and other mammals. Progress in understanding the mechanisms underlying the biology and the pathogenesis of <it>Histoplasma </it>has been hindered by a shortage of methodologies for mutating a gene of interest.</p> <p>Results</p> <p>We describe a reverse genetics process that combines the random mutagenesis of <it>Agrobacterium</it>-mediated transformation with screening techniques to identify targeted gene disruptions in a collection of insertion mutants. Isolation of the desired mutant is accomplished by arraying individual clones from a pool and employing a PCR-addressing method. Application of this procedure facilitated the isolation of a <it>cbp1 </it>mutant in a North American type 2 strain, a <it>Histoplasma </it>strain recalcitrant to gene knock-outs through homologous recombination. Optimization of cryopreservation conditions allows pools of mutants to be banked for later analysis and recovery of targeted mutants.</p> <p>Conclusion</p> <p>This methodology improves our ability to isolate mutants in targeted genes, thereby facilitating the molecular genetic analysis of <it>Histoplasma </it>biology. The procedures described are widely applicable to many fungal systems and will be of particular interest to those for which homologous recombination techniques are inefficient or do not currently exist.</p

Biochar as a cover for dairy manure lagoons: reducing odor and gas emissions while capturing nutrients

Liquid manure lagoons are known to be sources of odor and environmentally damaging gas emissions. Land application of the manure slurry after storage can lead to detrimental nutrient runoff and leaching. Floating lagoon covers (biocovers) are one option for reducing emissions, but to date they have only been used to address odors and emissions but not to address the problem of nutrient loss. This study evaluated the potential of floating biochar covers to reduce odor and gas emissions while simultaneously capturing nutrients from liquid dairy manure. The unique physical and chemical properties of biochars make them promising materials for odor, gas, and nutrient sorption. This new approach has the potential to mitigate multiple environmental problems. Two biochars were used to test this approach: one made from Douglas-fir chips under a low oxygen combustion environment at 650°C (FC650), and the other made from Douglas-fir hog fuel pyrolyzed at 600°C (HF600). The HF600 biocover reduced mean headspace ammonia (NH3) concentration by 7.5 to 13.6 μL/L. No significant reduction was found with the FC650 biocover. These biochars were able to sorb and hold nutrients while floating on the surface. Nutrient uptake by the two biochars ranged from 0.21 to 4.88 mg nitrogen g biochar-1 and 0.64 to 2.70 mg phosphorus g biochar-1. Potassium ranged from a loss of 4.52 to a gain of 2.65 mg g biochar-1. The biochars also sorbed calcium, magnesium, sodium, iron, aluminum, manganese, and silicon. In a separate experiment, a panel of judges evaluated the odor offensiveness (-10 to 10 scale) and odor threshold (1 to 10 scale) of five cover treatments including four biochars. Mean odor offensiveness ranged from -0.4 to -1.4 vs. -2.1 for the control. Mean odor threshold ranged from 1.6 to 2.1 vs. 2.6 for the control. These results show that biochar covers hold promise as an effective means for reducing odor and gas emissions while sorbing nutrients from liquid dairy manure. More research is needed to determine optimal biochar feedstock, production temperature, pH, and particle size distribution for use as a biocover material

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood. In addition, VarDict performs amplicon aware variant calling for polymerase chain reaction (PCR)-based targeted sequencing often used in diagnostic settings, and is able to detect PCR artifacts. Finally, VarDict also detects differences in somatic and loss of heterozygosity variants between paired samples. VarDict reprocessing of The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma dataset called known driver mutations in KRAS, EGFR, BRAF, PIK3CA and MET in 16% more patients than previously published variant calls. We believe VarDict will greatly facilitate application of NGS in clinical cancer research

Automated Reasoning for Multi-step Feature Model Configuration Problems

The increasing complexity and cost of software-intensive systems has led developers to seek ways of increasing software reusability. One software reuse approach is to develop a Software Product-line (SPL), which is a reconfigurable software architecture that can be reused across projects. Creating configurations of the SPL that meets arbitrary requirements is hard. Existing research has focused on techniques that produce a configuration of the SPL in a single step. This paper provides three contributions to the study of multi-step configuration for SPLs. First, we present a formal model of multi-step SPL configuration and map this model to constraint satisfaction problems (CSPs). Second, we show how solutions to these CSP configuration problem CSPs can be derived automatically with a constraint solver. Third, we present empirical results demonstrating that our CSP-based technique can solve multi-step configuration problems involving hundreds of features in seconds.Comisión Interministerial de Ciencia y Tecnología TIN2006-00472Junta de Andalucía TIC-253

Charge collection and trapping in low‐temperature silicon detectors

Charge collection efficiency measurements in silicon detectors at low temperature (T \u3c 0.5 K) and low applied electric field (E=0.1–100 V/cm) were performed using a variety of high‐purity, p‐type silicon samples with room‐temperature resistivity in the range 2–40 kΩ cm. Good charge collection under these conditions of low temperature and low electric field is necessary for background suppression, through the simultaneous measurement of phonons and ionization, in a very low event rate dark matter search or neutrino physics experiment. Charge loss due to trapping during drift is present in some samples, but the data suggest that another charge–loss mechanism is also important. We present results which indicate that, for 60 keV energy depositions, a significant fraction of the total charge loss by trapping occurs in the initial electron‐hole cloud near the event location which may briefly act as a shielded, field‐free region. In addition, measurements of the lateral size, transverse to the applied electric field, of the initial electron‐hole cloud indicate large transverse diffusion lengths. At the lowest fields a lateral diameter on the order of 1 mm is found in a detector ∼5 mm thick