Chemical bath deposition and electrodeposition of epitaxial semiconductor materials for application in photovoltaic devices

This dissertation investigates the chemical bath deposition of zinc oxide and electrodeposition of cuprous iodide on polycrystalline and single crystal substrates. Paper I describes the chemical bath deposition and characterization of titled epitaxial zinc oxide nanospears on Si(001) single crystal substrate. In Paper II, the chemical bath deposition of zinc oxide nanospears from highly alkaline solutions is discussed in detail, including a thermodynamic calculation of saturation and speciation of Zn(II) in aqueous solution, and a kinetic study of the deposition process. In this paper the epitaxial zinc oxide is reported grown on Au(100), (110), and (111) single crystals. Paper III involves the electrodeposition of epitaxial cuprous iodide thin films on single crystalline Au(100) substrate from a slightly acidic Cu(II)-EDTA-KI solution. The electronic property of the so deposited CuI film is estimated by photoluminescence spectroscopy. This dissertation also includes three appendices. The first two appendices cover the supplementary materials for Papers I and II. The third appendix has unpublished results on thermal transformation of electrodeposited magnetite and ferrihydrite into hematite --Abstract, page iv

Epitaxial Electrodeposition of Metal Oxide Thin Films and Superlattices for Energy Conversion and Storage

Track IV: Materials for Energy ApplicationsIncludes audio file (21 min.)Electrodeposition, like biomineralization, is a soft solution processing method in which inorganic materials are produced from solution precursors. The technique provides degrees of freedom that are not accessible to UHV deposition methods. The shape, orientation, and even chirality can be controlled through solution additives, pH, and electrode potential. Our emphasis is on producing epitaxial nanostructures of metal oxide semiconductors such as ZnO and Cu2O, magnetic materials such as Fe3O4, and battery materials such as LiMnO2. These materials are being produced for both the conversion and storage of energy. Cu2O is produced for photovoltaic devices and ZnO is produced for both photovoltaic devices and solid state lighting. Because the ZnO deposits as nanowires, electron-hole recombination can be minimized. We have recently found that ZnO can be epitaxially grown on single-crystal Si(111). In addition to exciton PL emission from the ZnO, there is also strong green emission due to native defects. Fe3O4 is being produced as thin films and superlattices for spintronic devices. Nanoribbons of LiMnO2 are deposited for use in high capacity lithium batteries. This material is presently used in Li batteries, but it is made by traditional powder metallurgy methods. The electrodeposition of nanostructured cathodes of this material could prove to be a major breakthrough in the lithium battery field

Selection of suitable reference genes for abiotic stress-responsive gene expression studies in peanut by real-time quantitative PCR

Background: Because of its strong specificity and high accuracy, real-time quantitative PCR (RT-qPCR) has been a widely used method to study the expression of genes responsive to stress. It is crucial to have a suitable set of reference genes to normalize target gene expression in peanut under different conditions using RT-qPCR. In this study, 11 candidate reference genes were selected and examined under abiotic stresses (drought, salt, heavy metal, and low temperature) and hormone (SA and ABA) conditions as well as across different organ types. Three statistical algorithms (geNorm, NormFinder and BestKeeper) were used to evaluate the expression stabilities of reference genes, and the comprehensive rankings of gene stability were generated. Results: The results indicated that ELF1B and YLS8 were the most stable reference genes under PEG-simulated drought treatment. For high-salt treatment using NaCl, YLS8 and GAPDH were the most stable genes. Under CdCl2 treatment, UBI1 and YLS8 were suitable as stable reference genes. UBI1, ADH3, and ACTIN11 were sufficient for gene expression normalization in low-temperature experiment. All the 11 candidate reference genes showed relatively high stability under hormone treatments. For organs subset, UBI1, GAPDH, and ELF1B showed the maximum stability. UBI1 and ADH3 were the top two genes that could be used reliably in all the stress conditions assessed. Furthermore, the necessity of the reference genes screened was further confirmed by the expression pattern of AnnAhs. Conclusions: The results perfect the selection of stable reference genes for future gene expression studies in peanut and provide a list of reference genes that may be used in the future

The Asian arowana (<i>Scleropages formosus</i>) genome provides new insights into the evolution of an early lineage of teleosts

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas

The Asian Arowana (Scleropages formosus) Genome Provides New Insights into the Evolution of an Early Lineage of Teleosts

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas

TransLiG: a de novo transcriptome assembler that uses line graph iteration

Abstract We present TransLiG, a new de novo transcriptome assembler, which is able to integrate the sequence depth and pair-end information into the assembling procedure by phasing paths and iteratively constructing line graphs starting from splicing graphs. TransLiG is shown to be significantly superior to all the salient de novo assemblers in both accuracy and computing resources when tested on artificial and real RNA-seq data. TransLiG is freely available at https://sourceforge.net/projects/transcriptomeassembly/files/

Tilted Epitaxial ZnO Nanospears on Si(001) by Chemical Bath Deposition

We show that epitaxial ZnO nanospears can be deposited onto degenerate p-type Si(001) from an alkaline supersaturated solution of Zn(II) at 70 °C using chemical bath deposition. The lattice mismatch between the hexagonal ZnO and-diamond cubic Si is reduced from -40.16% for an un-tilted structure to -0.25% in the ZnO[1210] direction and -0.99% in ZnO[2576] direction by tilting the nanospears 51° relative to the surface normal. The tilted nanostructure brings the (2023) planes of ZnO into coincidence with the (001) planes of Si. © 2009 American Chemical Society

Selection of suitable reference genes for abiotic stress-responsive gene expression studies in peanut by real-time quantitative PCR

Background: Because of its strong specificity and high accuracy, real-time quantitative PCR (RT-qPCR) has been a widely used method to study the expression of genes responsive to stress. It is crucial to have a suitable set of reference genes to normalize target gene expression in peanut under different conditions using RT-qPCR. In this study, 11 candidate reference genes were selected and examined under abiotic stresses (drought, salt, heavy metal, and low temperature) and hormone (SA and ABA) conditions as well as across different organ types. Three statistical algorithms (geNorm, NormFinder and BestKeeper) were used to evaluate the expression stabilities of reference genes, and the comprehensive rankings of gene stability were generated. Results: The results indicated that ELF1B and YLS8 were the most stable reference genes under PEG-simulated drought treatment. For high-salt treatment using NaCl, YLS8 and GAPDH were the most stable genes. Under CdCl2 treatment, UBI1 and YLS8 were suitable as stable reference genes. UBI1, ADH3, and ACTIN11 were sufficient for gene expression normalization in low-temperature experiment. All the 11 candidate reference genes showed relatively high stability under hormone treatments. For organs subset, UBI1, GAPDH, and ELF1B showed the maximum stability. UBI1 and ADH3 were the top two genes that could be used reliably in all the stress conditions assessed. Furthermore, the necessity of the reference genes screened was further confirmed by the expression pattern of AnnAhs. Conclusions: The results perfect the selection of stable reference genes for future gene expression studies in peanut and provide a list of reference genes that may be used in the future