Genome-wide high-resolution mapping of UV-induced mitotic recombination events in Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae and most other eukaryotes, mitotic recombination is important for the repair of double-stranded DNA breaks (DSBs). Mitotic recombination between homologous chromosomes can result in loss of heterozygosity (LOH). In this study, LOH events induced by ultraviolet (UV) light are mapped throughout the genome to a resolution of about 1 kb using single-nucleotide polymorphism (SNP) microarrays. UV doses that have little effect on the viability of diploid cells stimulate crossovers more than 1000-fold in wild-type cells. In addition, UV stimulates recombination in G1-synchronized cells about 10-fold more efficiently than in G2-synchronized cells. Importantly, at high doses of UV, most conversion events reflect the repair of two sister chromatids that are broken at approximately the same position whereas at low doses, most conversion events reflect the repair of a single broken chromatid. Genome-wide mapping of about 380 unselected crossovers, break-induced replication (BIR) events, and gene conversions shows that UV-induced recombination events occur throughout the genome without pronounced hotspots, although the ribosomal RNA gene cluster has a significantly lower frequency of crossovers

High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast.

In yeast, DNA breaks are usually repaired by homologous recombination (HR). An early step for HR pathways is formation of a heteroduplex, in which a single-strand from the broken DNA molecule pairs with a strand derived from an intact DNA molecule. If the two strands of DNA are not identical, there will be mismatches within the heteroduplex DNA (hetDNA). In wild-type strains, these mismatches are repaired by the mismatch repair (MMR) system, producing a gene conversion event. In strains lacking MMR, the mismatches persist. Most previous studies involving hetDNA formed during mitotic recombination were restricted to one locus. Below, we present a global mapping of hetDNA formed in the MMR-defective mlh1 strain. We find that many recombination events are associated with repair of double-stranded DNA gaps and/or involve Mlh1-independent mismatch repair. Many of our events are not explicable by the simplest form of the double-strand break repair model of recombination

The stabilization of repetitive tracts of DNA by variant repeats requires a functional DNA mismatch repair system

AbstractSimple repetitive tracts of DNA are unstable in all organisms thus far examined. In the yeast S. cerevisiae, we show that a 51 by poly(GT) tract alters length at a rate of about 10−5 per cell division. Insertion of a single variant repeat (either AT or CT) into the middle of the poly(GT) tract results in 100-fold stabilization. This stabilization requires the DNA mismatch repair system. Alterations within tracts with variant repeats occur more frequently on one side of the interruption than on the other. The stabilizing effects of variant repeats and polarity of repeat alterations have also been observed in trinucleotide repeats associated with certain human diseases

Impacts of Upstream Drought and Water Withdrawals on the Health and Survival of Downstream Estuarine Oyster Populations

Increases in the frequency, duration, and severity of regional drought pose major threats to the health and integrity of downstream ecosystems. During 2007-2008, the U.S. southeast experienced one of the most severe droughts on record. Drought and water withdrawals in the upstream watershed led to decreased freshwater input to Apalachicola Bay, Florida, an estuary that is home to a diversity of commercially and ecologically important organisms. This study applied a combination of laboratory experiments and field observations to investigate the effects of reduced freshwater input on Apalachicola oysters. Oysters suffered significant disease-related mortality under high-salinity, drought conditions, particularly during the warm summer months. Mortality was size-specific, with large oysters of commercially harvestable size being more susceptible than small oysters. A potential salinity threshold was revealed between 17 and 25 ppt, where small oysters began to suffer mortality, and large oysters exhibited an increase in mortality. These findings have important implications for watershed management, because upstream freshwater releases could be carefully timed and allocated during stressful periods of the summer to reduce disease-related oyster mortality. Integrated, forward-looking water management is needed, particularly under future scenarios of climate change and human population growth, to sustain the valuable ecosystem services on which humans depend

Haploidization in Saccharomyces cerevisiae Induced by a Deficiency in Homologous Recombination

Diploid Saccharomyes cerevisae strains lacking the RAD52 gene required for homologous recombination have a very high rate of chromosome loss. Two of four isolates subcultured ∼20 times (∼500 cell divisions) became haploid. These strains were capable of mating with wild-type haploids to produce diploid progeny capable of undergoing meiosis to produce four viable spores

Effects of environmental stress on intertidal mussel reproduction

Environmental stress can negatively affect the ability of organisms to reproduce. Energetic trade-offs exist in all organisms, and under stress, energy may be allocated away from reproduction and towards physiological defense and repair mechanisms. The rocky intertidal environment is ideal for investigating the influence of environmental stress, as organisms are exposed to both terrestrial and marine conditions due to tidal fluctuation. Aerial exposure at low tide can lead to high temperature, desiccation, and oxidative stress. Stress in the intertidal zone increases along a vertical gradient, as organisms in the high intertidal are exposed to air for longer periods of time than those in the low intertidal. Mussels are typically the dominant space-occupiers on temperate rocky shores, and they span the vertical gradient by occupying the entire mid-zone, from the low intertidal, which is a relatively low-stress environment, to the high intertidal, which is a high-stress environment. In this dissertation, we compared growth, reproduction, physiological defenses, pigmentation, and survival of mussels from the low-stress and high-stress regimes. We also compared energy allocation towards reproduction in mussels across a gradient of food availability between sites on the central Oregon coast. Findings indicate that growth and energy allocation towards reproduction are reduced in the high edge of the mussel bed, and physiological defenses are increased. A pattern was revealed where mussels in the high edge of the mussel bed are accumulating high concentrations of carotenoid pigments into their gonadal tissues, which was previously thought to be a secondary sex characteristic of females. This suggests that mussels may be incorporating carotenoids into their gonads in an effort to protect their gametes from damage by oxygen free radicals generated during aerial exposure. Results of this research have implications for intertidal systems under climate change scenarios, as extreme aerial temperature events are predicted to increase in frequency and severity, and changes in oceanic circulation may also occur. Based on the findings presented in this dissertation, increases in aerial temperature could potentially lead to decreased energy allocation towards reproduction, changes in spawning time, and reduced survival of adult mussels