This work examines the deposition of metallic and semiconductor elements onto self-assembled DNA templates for the fabrication of nanodevices. Biological molecules like DNA can self-assemble into a variety of complex 2-D and 3-D architectures without the need for expensive patterning tools. In addition, self-assembled DNA templates can be designed to controllably place functional nanomaterials with molecular precision. These characteristics make DNA an attractive template for fabricating electronic circuits from biological molecules. However, electrically conductive structures are required for electronic applications. While metallized DNA nanostructures have been demonstrated, the ability to make thin, continuous wires that are electrically conductive still represents a formidable challenge. DNA-templated wires have generally been granular in appearance with a resistivity approximately two to three orders of magnitude higher than that of the bulk material. An improved method for the metallization of DNA origami is examined in this work that addresses these challenges of size, morphology and conductivity of the metallized structure. Specifically, we demonstrated a metallization process that uses gold nanorod seeds followed by anisotropic electroless (autocatalytic) plating to provide improved morphology and greater control of the final metallized width of conducting metal lines. Importantly, growth during electroless deposition occurs preferentially in the length direction at a rate that is approximately four times the growth rate in the width direction, which enables fabrication of narrow, continuous wires. The electrical properties of 49 nanowires with widths ranging from 13 nm to 29 nm were characterized, and resistivity values as low as 8.9 x 10-7 Ω-m were measured, which represent some of the smallest nanowires and the lowest resistivity values reported in the literature. The metallization procedure developed on smaller templates was also successfully applied to metallize bigger DNA templates of tens of micrometers in length. In addition, a polymer-assisted annealing process was discovered to possibly improve the resistivity of DNA metal nanowires. Following metallization of bigger DNA origami structures, controlled placement of gold nanorods on a DNA breadboard (~100 x 100 nm2) to make rectangular, square and T-shaped metallic structures was also demonstrated. For site-specific placement of nanorods to a DNA template, we modified the surface of the gold nanorods with single-stranded DNA. The rods were then attached to DNA templates via complementary base-pairing between the DNA on the nanorods and the attachment strands engineered into the DNA "breadboard" template. Gaps between the nanorods were then filled controllably via anisotropic plating to make 10 nm diameter continuous metallic structures. Finally, controlled placement of metal (gold) - semiconductor (tellurium) materials on a single DNA origami template was demonstrated as another important step toward the fabrication of DNA-based electronic components. The combination of molecularly directed deposition and anisotropic metallization presented in this work represents important progress towards the creation of nanoelectronic devices from self-assembled biological templates.

This publication is the companion piece to “This Must Be the Place,” a 3D realization of my conceptual photography work exhibited in the Anderson Courtyard at VCU's 2019 School of the Arts MFA Show. I photograph scenes from nature and reproduce these images onto flattened plexiglass planes, arranging them in new, natural environments and photographing them again. The outcome is a scenic collage in which two unfamiliar locations become superimposed. It is my hope that as people experience the work they become a part of the texture of it.

Thesis (M.Sc. (Soil Science)) --University of Limpopo, 2013 / Large amount of pre-plant nitrogen (N) fertilizer results in low nutrient-use-efficiency due to poor synchrony between soil N supply and maize demand, especially during N sensitive growth stages. Optimum maize production is dependent on adequate N availability to the crop during the critical vegetative and reproductive growth stages. High N fertilizer prices and maize yield decline are the main challenges faced by the Limpopo Province farmers. The objectives of this study were to compare growth and yield of maize under conventional and site-specific N management in a dryland farming system. The study was conducted in Leeukraal, Towoomba, Ga-Marishane and Radium in the Limpopo Province, South Africa. Experimental plots were laid out in a randomized complete block design, with four replications. Phosphorus was applied through band placement using a planter in all plots at a rate of 42 kg P/ha. Hybrid maize SNK 2147 was planted on a 20 by 20 m plot with Inter-row and Intra-row spacing of 0.9 and 0.35 m respectively. Treatments consisted of 3 N management strategies as follows, (i) No N application (N0), (ii) Site-specific N at a rate ranging between 18 and 33 kg N/ha (N1) and (iii) Conventional N application at 58 kg N/ha (N2). Treatment N2 was applied at a uniform rate during maize planting. Sufficiency index as an indication for N deficiency was determined using CCM-200 for treatment N1. The sufficiency index was determined during leaf stage V6, V10 and V14, and thereafter N was applied only when needed. Data were subjected to analysis of variance through Statistical Analysis System package. Mean separation tests were computed using Duncan’s Multiple Range Test. Maize grain yield at Leeukraal of 5.2 t/ha for N1 was higher than 3.2 and 4.0 t/ha of N0 and N2, respectively. There was no difference amongst the three N management approaches on the grain yield at Towoomba. The grain yield at Ga-Marishane for N1 of 2.2 t/ha was significantly higher than 1.7 t/ha of the N0. Conventional management approach, which is a traditional approach used by farmers in the Limpopo Province, had 2.6 t/ha grain yield that was significantly higher than the N0 and N1. The maize growth and yield under N2 and N1 was compared, N1 required between 43 and 69% lesser N fertilizer as compared to N2. Therefore site-specific nutrient management approach sustains and improves growth and yield of maize using minimal inputs of N compared to conventional approach. This therefore saves input costs and avoids unnecessary environmental consequences. Key words: maize yield, nitrogen management, site-specific approach / Vlaamse Interuniveritatire Raad and Limpopo Department of Agriculture

Thesis (M.Sc. Agric (Soil Science)) -- University of Limpopo, 2013 / Knowledge and management of soil pH, particularly soil acidity across spatially variable soils is important, although this is greatly ignored by farmers in the Limpopo Province of South Africa. The significance of understanding spatial variability of soil acidity is the implementation of best and site-specific management strategies because when soil acidity is poorly managed, toxicity and nutrient deficiency problems in the soil are inevitable. The objective of the study was to evaluate in-field spatial variability of soil pH, and compare the efficiency of managing soil pH through site-specific method vs. uniform lime application. The study was conducted in 3 site years (23o50’ S; 29 o40’ E and 23o59’ S and 28o52’ E) with site year I, and II adjacent to each other in the semi-arid regions of the Limpopo Province, South Africa. Soil samples were taken in four replicates within a 1 m radius from geo-referenced locations in 3 study sites to sampling depths of 0-20 cm on a regular grid of 30m using differential Global Positioning System (DGPS). Soils were analyzed for pH, and SMP buffer pH for lime recommendations. Lime requirement to achieve a soil pH of 6.5 for a 20 cm plough layer per hectare was calculated using CalciumCarbonateequivalent, efficiency factor (fineness factor), and neutralizing index of the liming materials. The spatial maps for SMP buffer pH and lime requirement maps were produced with surfer version 8.0 (Surfer Version 8, Golden Software, Golden, CO). The soil pH datasets from systematic unaligned randomly sampled soils on a 30-m grid were interpolated using inverse distance weighing (IDW) in Surfer software version 8.0 (Surfer Version 8, Golden Software, Golden, CO). Soil pH varied from strongly acidic to slightly acidic with minimum values of 4.22, 3.93, and 4.74 and maximum values of 6.11, 7.00, and 6.82 in site I, II, and II respectively. In Site I, II, and III, the areas of the field that had soil pH values of less than 6.0 were 99.43, 82.61, and 62.89% of the field. When lime was recommended for application using a conventional method of uniform lime application based on an average value derived from samples collected in the whole field, the results of the study showed a waste of lime in excess of lime recommended for individual grids. An excess amount of lime as high as 10, 30, and 7 tons/ha recommended on sites I, II and III respectively under uniform application. These recommendations were in excess on field areas that needed little or no lime applications. Again, the fields showed under applications of lime as much as 30, 35, and 13 tons/ha in site I, II, and III respectively for uniform liming applications. This under- and over recommendations of lime based on average soil pH values suggests that uniform soil acidity management strategy is not an appropriate strategy to be adopted in these fields. Again, in both of these sites as shown in the maps, the areas that required high amount of lime and those that require little or no lime are clearly defined, such that the fields can be divided into lime application zones. When a field is divided into lime application zones, management of soil acidity becomes easier because instead of applying variable rates of lime for every grid, lime rates are applied per zone. These zones could be areas in a field that require, (i) high rates of lime, (ii) low rates of lime, and (iii) areas that requires no lime at all. Agricultural fields that exhibit spatial variability of soil acidity must not be managed or treated as uniform when lime is applied in the field. Keywords: Lime requirement, Site specific management and Soil pH.

<p>Bacterial resistance to antibiotics has become a serious problem. This is due to the remarkable ability of bacteria to respond and rapidly adapt to environmental changes. Integrons are elements with the capacity for gene capture by an integron-encoded site-specific recombinase called IntI. IntI binds and acts at the recombination sites, <i>attI </i>and<i> attC</i> resulting in excision and integration of short DNA elements called gene cassettes carrying an <i>attC</i> site in the 3’ end. Several families of antibiotic resistance genes are borne on gene cassettes in integrons connected to mobile elements. Other cassettes reside in the larger and ancestral superintegrons located on chromosomes in both pathogenic and environmental bacteria. Due to their close connection with lateral gene transfer systems, it is possible that integrons are functionally dependent on those networks. This work presents arguments for such connections. The<i> attC</i> of the <i>aadA1-qacE</i> cassette junction in Tn<i>21</i> was characterized in detail. Like other <i>attC</i> sites, it contains two pairs of inverted repeats and is almost palindromic. By using electrophoretic mobility shift assays, this study showed that IntI1 binds only to the bottom strand of <i>attC</i>. Upon folding the strand into a hairpin, a few chiral hairpin distortions define both the strand choice and also the appropriate orientation of the highly symmetrical site. Structural recognition also explains the wide sequence variation among <i>attC</i> sites. We have documented the initial cleavage step in recombination in IntI extracts and integrase levels in extracts were evaluated by a new method. Mutagenesis and homology modelling were performed to find amino acid residues in IntI1 that are important for recognition of <i>attC</i> hairpin-DNA. Comparisons were made with other tyrosine family members to explain how integron integrases differ in site-recognition and also in their mechanism of strand exchange.</p>

Genetic engineering is important to enhance crop characteristics and certain traits. Genetically engineered crop cultivation brings environmental and ecological concerns with the potential of unwanted transgene escape and introgression. Transgene escape has been considered as a major environmental and regulatory concern. This concern could be alleviated by appropriate biocontainment strategies. Therefore, it is important to develop efficient and reliable biocontainment strategies. Removing transgenes from pollen has been known to be the most environmentally friendly biocontainment strategy. A transgene excision vector containing a codon optimized serine resolvase CinH recombinase (CinH) and its recognition sites RS2 were constructed and transformed into tobacco (Nicotiana tabacum cv. Xanthi). In this system, the pollen-specific LAT52 promoter from tomato was employed to control the expression of CinH recombinase. Loss of expression of a green fluorescent protein (GFP) gene under the control of the LAT59 promoter from tomato was used as an indicator of transgene excision. Efficiency of transgene excision from pollen was determined by flow cytometry (FCM)-based pollen screening. While a transgenic event in the absence of CinH recombinase contained about 70% of GFP-synthesizing pollen, three single-copy transgene events contained less than 1% of GFP-synthesizing pollen based on 30,000 pollen grains analyzed per event. This suggests that CinH-RS2 recombination system could be effectively utilized for transgene biocontainment. A novel approach for selective male sterility in pollen was developed and evaluated as a biocontainment strategy. Overexpression of the EcoRI restriction endonuclease caused pollen ablation and/or infertility in tobacco, but exhibited normal phenotypes when compared to non-transgenic tobacco. Three EcoRI contained 0% GFP positive pollen, while GFP control plants contained 64% GFP positive pollen based on 9,000 pollen grains analyzed by flow cytometry-based transgenic pollen screening method. However, seven EcoRI events appeared to have 100% efficiency on selective male sterility based on the test-crosses. The results suggested that this selective male sterility could be used as a highly efficient and reliable biocontainment strategy for genetically engineered crop cultivation.

Bacterial resistance to antibiotics has become a serious problem. This is due to the remarkable ability of bacteria to respond and rapidly adapt to environmental changes. Integrons are elements with the capacity for gene capture by an integron-encoded site-specific recombinase called IntI. IntI binds and acts at the recombination sites, attI and attC resulting in excision and integration of short DNA elements called gene cassettes carrying an attC site in the 3’ end. Several families of antibiotic resistance genes are borne on gene cassettes in integrons connected to mobile elements. Other cassettes reside in the larger and ancestral superintegrons located on chromosomes in both pathogenic and environmental bacteria. Due to their close connection with lateral gene transfer systems, it is possible that integrons are functionally dependent on those networks. This work presents arguments for such connections. The attC of the aadA1-qacE cassette junction in Tn21 was characterized in detail. Like other attC sites, it contains two pairs of inverted repeats and is almost palindromic. By using electrophoretic mobility shift assays, this study showed that IntI1 binds only to the bottom strand of attC. Upon folding the strand into a hairpin, a few chiral hairpin distortions define both the strand choice and also the appropriate orientation of the highly symmetrical site. Structural recognition also explains the wide sequence variation among attC sites. We have documented the initial cleavage step in recombination in IntI extracts and integrase levels in extracts were evaluated by a new method. Mutagenesis and homology modelling were performed to find amino acid residues in IntI1 that are important for recognition of attC hairpin-DNA. Comparisons were made with other tyrosine family members to explain how integron integrases differ in site-recognition and also in their mechanism of strand exchange.

A portable dual-camera video system was used to evaluate the potential for using total projected green cover as an indirect measure of weed infestations in a wheat crop during early growth stages. The video system would have applications in mapping weed infestations to assist precision farming operations. <p>The two cameras provided a real-time composite image of reflected light measured in red (640 nm), and near-infrared (860 nm) wavelengths. A simple ratio of reflected light intensity in each wavelength was used to isolate the growing plants from the background. Software was developed to automatically adjust for varying ambient light conditions and calculate the percentage of the image occupied by growing plants. Total green cover was measured at randomly selected sites prior to direct seeding wheat and at four growth stages following wheat emergence. The portion of green cover observed was compared to crop and weed dry matter at each location. Weed infestations at each location were estimated by measuring the total green cover and subtracting the projected green cover due to the crop alone. A minimum weed dry matter of 20 g/m2 and 30 g/m2 could be detected by the video system at the 3-leaf and 5-leaf growth stages, respectively. Weed dry matter less than 20 g/m2 could not be detected reliably due to the variability of the wheat crop. Detection of weeds within the crop beyond the 5-leaf stage using this method was difficult due to crop canopy closure.

The work describes the development of a new class of synthetic metallopeptides that features a dirhodium metal center. Combination of peptide and dirhodium properties leads to unique effects on peptide structure, peptide-protein interactions, and metal catalytic activity aimed at small molecule as well as protein substrates. Dirhodium is directly bound to carboxylate side chains of aspartate or glutamate yielding kinetically inert coordination complexes. This improves stability, allows purification and provides enhanced biocompatibility. Bridging of two side chains in the same sequence enables control of the peptide secondary structure. Dirhodium metallopeptides are applied to regulate coiled coil dimerization, stabilize and induce helical secondary structure, catalyze enantioselective organometallic transformation, and serve as ligands for proteins. These results lead to the development of hybrid organic-inorganic therapeutic agents, biological probes for study of protein-protein interactions, and enantioselective metallopeptide catalysis.

A portable dual-camera video system was used to evaluate the potential for using total projected green cover as an indirect measure of weed infestations in a wheat crop during early growth stages. The video system would have applications in mapping weed infestations to assist precision farming operations. <p>The two cameras provided a real-time composite image of reflected light measured in red (640 nm), and near-infrared (860 nm) wavelengths. A simple ratio of reflected light intensity in each wavelength was used to isolate the growing plants from the background. Software was developed to automatically adjust for varying ambient light conditions and calculate the percentage of the image occupied by growing plants. Total green cover was measured at randomly selected sites prior to direct seeding wheat and at four growth stages following wheat emergence. The portion of green cover observed was compared to crop and weed dry matter at each location. Weed infestations at each location were estimated by measuring the total green cover and subtracting the projected green cover due to the crop alone. A minimum weed dry matter of 20 g/m2 and 30 g/m2 could be detected by the video system at the 3-leaf and 5-leaf growth stages, respectively. Weed dry matter less than 20 g/m2 could not be detected reliably due to the variability of the wheat crop. Detection of weeds within the crop beyond the 5-leaf stage using this method was difficult due to crop canopy closure.