Kinetic modeling of microscopic processes during electron cyclotron resonance microwave plasma-assisted molecular beam epitaxial growth of GaN/GaAs-based heterostructures

Microscopic growth processes associated with GaN/GaAs molecular beam epitaxy (MBE) are examined through the introduction of a first-order kinetic model. The model is applied to the electron cyclotron resonance microwave plasma-assisted MBE (ECR-MBE) growth of a set of delta-GaNyAs1–y/GaAs strained-layer superlattices that consist of nitrided GaAs monolayers separated by GaAs spacers, and that exhibit a strong decrease of y with increasing T over the range 540–580 °C. This y(T) dependence is quantitatively explained in terms of microscopic anion exchange, and thermally activated N surface-desorption and surface-segregation processes. N surface segregation is found to be significant during GaAs overgrowth of GaNyAs1–y layers at typical GaN ECR-MBE growth temperatures, with an estimated activation energy Es ~ 0.9 eV. The observed y(T) dependence is shown to result from a combination of N surface segregation/desorption processes

Transforming Tertiary Science Education: Improving learning during lectures

Science education research shows that a traditional, stand-and-deliver lecture format is less effective than teaching strategies that are learner-centred and that promote active engagement. The Carl Wieman Science Education Initiative (CWSEI) has used this research to develop resources to improve learning in university science courses. We report on a successful adaptation and implementation of CWSEI in the New Zealand university context. This two-year project at Massey University and the University of Canterbury began by using perception and concept surveys before and after undergraduate science courses to measure students’ attitudes towards science as well as their knowledge. Using these data, and classroom observations of student engagement and corroborating focus groups, the research team worked with lecturers to create interventions to enhance student engagement and learning in those courses. Results show several positive changes related to these interventions and they suggest several recommendations for lecturers and course coordinators. The recommendations include:1. Make learning outcomes clear, both for the lecturer and the students; this helps to cull extraneous material and scaffold student learning. 2. Use interactive activities to improve engagement, develop deeper levels of thinking, and improve learning. 3. Intentionally foster “expert-like thinking” amongst students in the first few semesters of the degree programme. 4. Be flexible because one size does not fit all and contextual events are beyond anyone’s control.In addition to these recommendations, data collected at the Canterbury site during the 2010 and 2011 earthquakes reinforced the understanding that the most carefully designed teaching innovations are subject to contextual conditions beyond the control of academics

Operating Cooperatively (OC) Sensor for Highly Specific Recognition of Nucleic Acids

<div><p>Molecular Beacon (MB) probes have been extensively used for nucleic acid analysis because of their ability to produce fluorescent signal in solution instantly after hybridization. The indirect binding of MB probe to a target analyte offers several advantages, including: improved genotyping accuracy and the possibility to analyse folded nucleic acids. Here we report on a new design for MB-based sensor, called ‘<i>Operating Cooperatively’</i> (OC), which takes advantage of indirect binding of MB probe to a target analyte. The sensor consists of two unmodified DNA strands, which hybridize to a universal MB probe and a nucleic acid analyte to form a fluorescent complex. OC sensors were designed to analyze two human SNPs and <i>E.coli</i> 16S rRNA. High specificity of the approach was demonstrated by the detection of true analyte in over 100 times excess amount of single base substituted analytes. Taking into account the flexibility in the design and the simplicity in optimization, we conclude that OC sensors may become versatile and efficient tools for instant DNA and RNA analysis in homogeneous solution.</p> </div

Detection of bacterial 16S rRNA with OC sensor.

<p>A) Signal-to-noise ratios for OC sensor detection of various concentrations of <i>E. coli</i> 16S rRNA in vitro transcript. Average signal-to-noise (S/N) values of three independent measurements with a standard deviation are presented. B) Fluorescent spectra of OC sensor detection of 16S rRNA from bacteria total RNA isolation. The assays were conducted in 50 mM Tris HCl, pH 7.4, 50 mM MgCl₂ with a 5 minute annealing step (90°C) followed by 15 minute incubation at room temperature (22°C).</p

Limit of detection (LOD) for the OC sensor.

<p><i>O1, C1,</i> and UMB1 probe were used to analyze low concentrations of the matched analyte (rs87T). The limit of detection (LOD) was calculated as the analyte concentration that triggered a fluorescent signal equal to the average fluorescence of the background from three independent measurements plus three standard deviations of the average background fluorescence. Data shown were plotted as the mean with error bars representing one standard deviation from the mean from three independent trials. LOD was determined in the absence (blue line) or in the presence (red line) of 500 nM of mismatched analyte (rs87C). The green dashed lines represent the respective thresholds and the black dashed lines represent the respective LODs.</p

OC sensor for detection of secondary structure-forming fragment of <i>E.coli</i> 16S rRNA.

<p>A) Sequences and the predicted secondary structure of stem-loop folded fragments of 16S rRNA. The nucleotide variations in <i>E. coli</i> and <i>B. subtilis</i> 16S rRNA are shown in magenta. B) OC sensor in the complex with fully matched <i>E.coli f-1</i> sequence. MB binding arms of strands <i>O2</i> and <i>C2</i> are shown in cyan. C) Signal-to-noise ratio of fluorescent response of OC sensor in the presence of absence of <i>E.coli</i> or <i>B. subtilis</i> 16S rRNA mimics. The assay was conducted in 50 mM Tris HCl, pH 7.4, 50 mM MgCl₂ at room temperature (22°C). The data represents the signal to noise ratios of three independent experiments with error bars indicating one standard deviation from the mean.</p

Oligonucleotides used in the study.

*<p>Polymorphic sites are underlined.</p

OC sensor for SNP-selective nucleic acid analysis.

<p>A) Sensor in complex with rs87T analyte and UMB1 probe. The sensor was designed to recognize the thymidine containing allele, while discriminating against the alternative cytosine containing allele. MB-binding arms are shown in cyan. B) Fluorescent response of OC sensor specific to rs87T allele sequence in the absence or presence of specific or non-specific analytes. C) Signal-to-noise ratios of four independent experiments with error bars indicating one standard deviation from the mean. The complete sequences of all oligonucleotides are included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055919#pone-0055919-t001" target="_blank">Table 1</a>.</p

Molecular beacon-based sensors for nucleic acid detection.

<p>A) Conventional MB probe <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055919#pone.0055919-Tyagi1" target="_blank">[9]</a>. B) MB-based binary DNA sensor (BDS) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055919#pone.0055919-Gerasimova1" target="_blank">[32]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055919#pone.0055919-Gerasimova2" target="_blank">[34]</a>. Dashed lines indicate triethylene glycol linkers. C) DX-tile based sensor <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055919#pone.0055919-Kolpashchikov3" target="_blank">[35]</a>. D) OC sensor used in this study.</p