Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum

To better understand the evolution of mitochondrial (mt) genomes in the Acari (mites and ticks), we sequenced the mt genome of the chigger mite, Leptotrombidium pallidum (Arthropoda: Acari: Acariformes). This genome is highly rearranged relative to that of the hypothetical ancestor of the arthropods and the other species of Acari studied. The mt genome of L. pallidum has two genes for large subunit rRNA, a pseudogene for small subunit rRNA, and four nearly identical large noncoding regions. Nineteen of the 22 tRNAs encoded by this genome apparently lack either a T-arm or a D-arm. Further, the mt genome of L. pallidum has two distantly separated sections with identical sequences but opposite orientations of transcription. This arrangement cannot be accounted for by homologous recombination or by previously known mechanisms of mt gene rearrangement. The most plausible explanation for the origin of this arrangement is illegitimate inter-mtDNA recombination, which has not been reported previously in animals. In light of the evidence from previous experiments on recombination in nuclear and mt genomes of animals, we propose a model of illegitimate inter-mtDNA recombination to account for the novel gene content and gene arrangement in the mt genome of L. pallidum.

STAR: predicting recombination sites from amino acid sequence

Background: Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probability that hybrid sequences have the desired properties is increased dramatically. The prohibitive requirements for applying current tools led us to investigate machine learning to assist in finding useful recombination sites from amino acid sequence alone. Results: We present STAR, Site Targeted Amino acid Recombination predictor, which produces a score indicating the structural disruption caused by recombination, for each position in an amino acid sequence. Example predictions contrasted with those of alternative tools, illustrate STAR'S utility to assist in determining useful recombination sites. Overall, the correlation coefficient between the output of the experimentally validated protein design algorithm SCHEMA and the prediction of STAR is very high (0.89). Conclusion: STAR allows the user to explore useful recombination sites in amino acid sequences with unknown structure and unknown evolutionary origin. The predictor service is available from http://pprowler.itee.uq.edu.au/star.

Three-body recombination of ultracold Bose gases using the truncated Wigner method

We apply the truncated Wigner method to the process of three-body recombination in ultracold Bose gases. We find that within the validity regime of the Wigner truncation for two-body scattering, three-body recombination can be treated using a set of coupled stochastic differential equations that include diffusion terms, and can be simulated using known numerical methods. As an example we investigate the behavior of a simple homogeneous Bose gas, finding a very slight increase of the loss rate compared to that obtained by using the standard method.

Determination of recombination coefficients for nanocrystalline silicon embedded in hydrogenated amorphous silicon

The spectroscopic pump-probe reflectance method was used to investigate recombination dynamics in samples of nanocrystalline silicon embedded in a matrix of hydrogenated amorphous silicon. We found that the dynamics can be described by a rate equation including linear and quadratic terms corresponding to recombination processes associated with impurities and impurity-assisted Auger ionization, respectively. We determined the values of the recombination coefficients using the initial concentrations method. We report the coefficients of 1.5 × 1011 s-1 and 1.1 × 10-10 cm3 s-1 for the impurity-assisted recombination and Auger ionization, respectively.

Experiments in the dissociative recombination of xenon and krypton

Experiments were conducted using the Time of Flight (TOF) method to identify the final product states of the dissociative recombination reaction of krypton and xenon. In the dissociative recombination (DR) reaction the molecular ion breaks up into product atoms whose velocities can be measured. These velocities can then be used to identify the final product states. The DR of krypton had been studied by Shiu and Biondi using spectrometric techniques. They observed the 5p states. Hardy et al. using TOF techniques had observed the 5s states. Mitchell et al. studied the DR of xenon. They observed the 6p and 5d states of xenon. In this laboratory using the TOF method I have recently identified the 5s, 6p and the 4d final states of the DR of krypton. Then I was able to identify the 5d, 7s, 6d, and 6p′ final product states of the DR of xenon. The study of the DR of these heavy inert gases can shed light on the theory of the DR of heavy polyatomic gases, which is not well developed. ^

Investigation of generation -recombination noise and related processes in aluminum gallium arsenide TEGFETs and Hall structures with quantum wells

Experimental and theoretical studies regarding noise processes in various kinds of AlGaAs/GaAs heterostructures with a quantum well are reported. The measurement processes, involving a Fast Fourier Transform and analog wave analyzer in the frequency range from 10 Hz to 1 MHz, a computerized data storage and processing system, and cryostat in the temperature range from 78 K to 300 K are described in detail. The current noise spectra are obtained with the “three-point method”, using a Quan-Tech and avalanche noise source for calibration. ^ The properties of both GaAs and AlGaAs materials and field effect transistors, based on the two-dimensional electron gas in the interface quantum well, are discussed. Extensive measurements are performed in three types of heterostructures, viz., Hall structures with a large spacer layer, modulation-doped non-gated FETs, and more standard gated FETs; all structures are grown by MBE techniques. ^ The Hall structures show Lorentzian generation-recombination noise spectra with near temperature independent relaxation times. This noise is attributed to g-r processes in the 2D electron gas. For the TEGFET structures, we observe several Lorentzian g-r noise components which have strongly temperature dependent relaxation times. This noise is attributed to trapping processes in the doped AlGaAs layer. The trap level energies are determined from an Arrhenius plot of log (τT2) versus 1/T as well as from the plateau values. The theory to interpret these measurements and to extract the defect level data is reviewed and further developed. Good agreement with the data is found for all reported devices. ^

Genetic Analysis of Mitotic Recombination in Saccharomyces cerevisiae

Mitotic genome instability can occur during the repair of double-strand breaks (DSBs) in DNA, which arise from endogenous and exogenous sources. Studying the mechanisms of DNA repair in the budding yeast, Saccharomyces cerevisiae has shown that Homologous Recombination (HR) is a vital repair mechanism for DSBs. HR can result in a crossover event, in which the broken molecule reciprocally exchanges information with a homologous repair template. The current model of double-strand break repair (DSBR) also allows for a tract of information to non-reciprocally transfer from the template molecule to the broken molecule. These “gene conversion” events can vary in size and can occur in conjunction with a crossover event or in isolation. The frequency and size of gene conversions in isolation and gene conversions associated with crossing over has been a source of debate due to the variation in systems used to detect gene conversions and the context in which the gene conversions are measured.

In Chapter 2, I use an unbiased system that measures the frequency and size of gene conversion events, as well as the association of gene conversion events with crossing over between homologs in diploid yeast. We show mitotic gene conversions occur at a rate of 1.3x10-6 per cell division, are either large (median 54.0kb) or small (median 6.4kb), and are associated with crossing over 43% of the time.

DSBs can arise from endogenous cellular processes such as replication and transcription. Two important RNA/DNA hybrids are involved in replication and transcription: R-loops, which form when an RNA transcript base pairs with the DNA template and displaces the non-template DNA strand, and ribonucleotides embedded into DNA (rNMPs), which arise when replicative polymerase errors insert ribonucleotide instead of deoxyribonucleotide triphosphates. RNaseH1 (encoded by RNH1) and RNaseH2 (whose catalytic subunit is encoded by RNH201) both recognize and degrade the RNA in within R-loops while RNaseH2 alone recognizes, nicks, and initiates removal of rNMPs embedded into DNA. Due to their redundant abilities to act on RNA:DNA hybrids, aberrant removal of rNMPs from DNA has been thought to lead to genome instability in an rnh201Δ background.

In Chapter 3, I characterize (1) non-selective genome-wide homologous recombination events and (2) crossing over on chromosome IV in mutants defective in RNaseH1, RNaseH2, or RNaseH1 and RNaseH2. Using a mutant DNA polymerase that incorporates 4-fold fewer rNMPs than wild type, I demonstrate that the primary recombinogenic lesion in the RNaseH2-defective genome is not rNMPs, but rather R-loops. This work suggests different in-vivo roles for RNaseH1 and RNaseH2 in resolving R-loops in yeast and is consistent with R-loops, not rNMPs, being the the likely source of pathology in Aicardi-Goutières Syndrome patients defective in RNaseH2.

RECQ5 promotes recombination and mutagenesis at targeted nicks through disruption of RAD51 filaments

Thesis (Ph.D.)--University of Washington, 2016-08

'On the Application of Hierarchical Coevolutionary Genetic Algorithms: Recombination and Evaluation Partners'

This paper examines the use of a hierarchical coevolutionary genetic algorithm under different partnering strategies. Cascading clusters of sub-populations are built from the bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations potentially search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the sub-populations on solution quality are examined for two constrained optimisation problems. We examine a number of recombination partnering strategies in the construction of higher-level individuals and a number of related schemes for evaluating sub-solutions. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.