The influence of ion energy, ion flux, and etch temperature on the electrical and material quality of GaAs etched with an electron cyclotron resonance source

The residual damage incurred to GaAs via etching with a Cl2/Ar plasma generated by an electron cyclotron resonance (ECR) source was investigated as a function of variations in ion energy, ion flux, and etching temperature. The residual damage and electrical properties of GaAs were strongly influenced by changes in these etching parameters. Lattice damage was incurred in all processing situations in the form of small dislocation loops. GaAs etched at high ion energies with 200 W rf power, exhibited a defect density five times higher than GaAs etched at lower ion energies with 20 W rf power. This enhanced residual damage at the higher rf powers was paralleled by a degradation in the unannealed contact resistance. Higher etch rates, which accompany the higher rf power levels, caused the width of the disordered region to contract as the rf power was elevated. Therefore, the residual etch damage is influenced by both the generation and removal of defects. Increasing the microwave power or ion flux resulted in elevating the residual defect density, surface roughness, and unannealed contact resistance. GaAs etched at high temperatures, ∼350 °C, resulted in a lower contact resistance than GaAs etched at 25 °C. The high temperature etching augmented the defect diffusion which in turn lowered the near surface defect density. This decrease in residual damage was deemed responsible for improving the electrical performance at 350 °C. The electrical measurements were found to be more sensitive to the density of defects than the vertical extent of disorder beneath the etched surface. Results of this investigation demonstrate that in order to minimize material damage and improve electrical performance, etching with an ECR source should be performed at low rf and microwave powers with a high substrate temperature. © 1995 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70988/2/JAPIAU-78-4-2712-1.pd

Isolation and characterization of tomato cDNA and genomic clones encoding the ubiquitin gene ubi3

We report here the isolation and nucleotide sequence of tomato cDNA and genomic clones encoding a ubiquitin extension protein homologous to the yeast gene ubi3 . Sites similar to upstream activating sites commonly found in the promoters of yeast ribosomal genes were observed in the tomato promoter. The tomato ubi3 promoter also contained elements found in the rbcS promoter from pea. The transcription initiation site was determined to occur 66 bp upstream of the initiating Met. RFLP mapping revealed that the gene was located on chromosome 1, 23 cM from marker TG301. A ubi3 gene-specific probe hybridized to a single 800 nt transcript. Expression was reduced in heat-shocked plants and plants kept in the dark. Expression was highest in young leaves and immature green fruit and lowest in mature leaves and petals. We isolated the original cDNA clone using an antibody prepared against chloroplast polypeptides. Immunological studies did not detect ubiquitin or ubiquitin extension proteins in the chloroplast. However, higher-molecular-weight chloroplast proteins were detected with ubiquitin antisera suggesting that ubiquitin conjugates are transported into the chloroplast.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43430/1/11103_2004_Article_BF00028735.pd

Electronic properties of GaAs surfaces etched in an electron cyclotron resonance source and chemically passivated using P2S5P2S5

Photoreflectance has been used to study the electronic properties of (100) GaAs surfaces exposed to a Cl2/ArCl2/Ar plasma generated by an electron cyclotron resonance source and subsequently passivated by P2S5.P2S5. The plasma etch shifts the Fermi level of p-GaAsp-GaAs from near the valence band to midgap, but has no effect on n-GaAs.n-GaAs. For ion energies below 250 eV, post-etch P2S5P2S5 chemical passivation removes the surface etch damage and restores the electronic properties to pre-etch conditions. Above 250 eV, the etch produces subsurface defects which cannot be chemically passivated. Auger electron spectroscopy shows that etching increases As at the GaAs/oxide interface, while passivation reduces it. © 1998 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69373/2/APPLAB-73-1-114-1.pd

Potential for Mcl-PHA Production from Nonanoic and Azelaic Acids

Greater than 65 % of canola and high oleic soy oil fatty acids is oleic acid, which is readily converted to nonanoic (NA) and azelaic (AzA) acids by ozonolysis. NA is an excellent substrate for medium-chain-length polyhydroxyalkanoate (mcl-PHA) production but AzA has few uses. Pseudomonas citronellolis DSM 50332 and Pseudomonas fluorescens ATCC 17400, both able to produce mcl-PHA from fatty acids and able to grow on AzA as the sole source of carbon and energy were assessed for the accumulation of mcl-PHA from AzA and NA. In N-limited shake-flasks using NA, P. citronellolis produced 32% of its dry biomass as mcl-PHA containing 78% 3-hydroxynonanoate with 22 % 3-hydroxyheptanoate. P. fluorescens produced only 2% PHA.. N-limited P. citronellolis on AzA produced 20% dry weight PHA containing 75% 3-hydroxydecanoate and 25% 3-hydroxyoctanoate, indicative of de novo synthesis. Although selective pressure, including β-oxidation inhibition, under well-controlled (chemostat) conditions was applied to P. citronellolis, no side-chain carboxyl groups were detected. It was concluded that one or more of FabG and PhaJ or the PHA synthase cannot catalyze reactions involving Ď -carboxy substrates. However, a process based on oleic acid could be established if P. putida was engineered to grow on AzA.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs

High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline optimized for rRNA- and tRNA-derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users’ input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0. Keywords: Small RNA, RNA-seq data analysis, tsRNA, rsRNA, Annotation pipelin

SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs.

High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipelineoptimized for rRNA- and tRNA-derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users' input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0

Effects of electron cyclotron resonance etching on the ambient (100) GaAs surface

Photoreflectance has been used to study the electronic behavior of the ambient (100) GaAs surface and its modification by etching in a Cl2/Ar plasma generated by an electron‐cyclotron resonance (ECR) source. We observed two pinning positions for ambient (100) GaAs, with n‐GaAs pinning near midgap and p‐GaAs pinning near the valance band. ECR etching shifts the Fermi level of p‐GaAs toward midgap, but has little effect on n‐GaAs. The surface modification is most influenced by the rf power. Auger electron spectroscopy indicates that the etching increases As at the GaAs/oxide interface. We suggest that the Ga/As ratio controls the position of the Fermi level. © 1995 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69627/2/APPLAB-66-22-3054-1.pd

Photoluminescence and electro‐optic properties of small (25–35 nm diameter) quantum boxes

The luminescence and electro‐optic properties of buried 25–35 nm quantum boxes have been measured. The quantum boxes were defined by a combination of molecular beam epitaxial growth and regrowth, electron beam lithography, and dry etching. The photoluminescence from 35 nm boxes shows a blue shift of ∼15 meV compared to the bulk luminescence and an enhancement, taking into account the fill factor. An enhanced effective linear electro‐optic coefficient, rl, is observed for the quantum boxes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69405/2/APPLAB-62-22-2766-1.pd

Microtubule structures underlying the sarcoplasmic reticulum support peripheral coupling sites to regulate smooth muscle contractility

Microtubules position ion channels close to each other to ensure autoregulation of vascular tone in cerebral arteries.</jats:p