Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 in : A Budding Yeast in Distress.

The industrially important non-conventional yeast suffers from low rates of homologous recombination, making site specific genetic engineering tedious. Therefore, genome editing using CRISPR/Cas represents a simple and efficient alternative. To characterize on- and off-target mutations caused by CRISPR/Cas9 followed by non-homologous end joining repair, we chose a diverse set of CRISPR/Cas targets and conducted whole genome sequencing on 146 CRISPR/Cas9 engineered single colonies.

Apomixis and genetic background affect distinct traits in Hieracium pilosella L. grown under competition.

Background: Apomixis, the asexual reproduction through seeds, occurs in over 40 plant families and avoids the hidden cost of sex. Apomictic plants are thought to have an advantage in sparse populations and when colonizing new areas but may have a disadvantage in changing environments because they propagate via fixed genotypes. In this study, we separated the influences of different genetic backgrounds (potentially reflecting local adaptation) from those of the mode of reproduction, i.

Dynamics of apomictic and sexual reproduction during primary succession on a glacier forefield in the Swiss Alps.

Apomixis, the asexual reproduction through seeds, is thought to provide reproductive assurance when ploidy is not even and/or when population density is low. Therefore, apomicts are expected to be more abundant, and the frequency of apomictic offspring higher, at early stages of primary succession when mates are rare. To test this hypothesis, we sampled facultative apomictic Hieracium pilosella L.

Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils.

It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium.

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa.

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ~300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species.

Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils.

When plants adapt to local environments, strong signatures of selection are expected in the genome, particularly in high-stress environments such as trace metal element enriched (metalliferous) soils. Using Arabidopsis halleri, a model species for metal homeostasis and adaptation to extreme environments, we identifid genes, gene variants, and pathways that are associated with soil properties and may thus contribute to adaptation to high concentrations of trace metal elements. We analysed whole-genome Pool-seq data from two metallicolous (from metalliferous soils) and two non-metallicolous populations (in total 119 individuals) and associated allele frequencies of the identified single-nucleotide polymorphisms (SNPs) with soil variables measured on site.

Apomixis Allows the Transgenerational Fixation of Phenotypes in Hybrid Plants.

The introduction of apomixis-asexual reproduction through seeds-into crop plants is considered the holy grail of agriculture, as it would provide a mechanism to maintain agriculturally important phenotypes [1, 2]. Apomicts produce clonal offspring, such that apomixis could be used to transgenerationally fix any genotype, including that of F1 hybrids, which are used in agriculture due to their superior vigor and yield [3-9]. However, traits (phenotypes) do not only result from a complex combination of genetic and environmental variation but can also be influenced by epigenetic variation, which can be transgenerationally heritable in plants [10-15].

Parental age affects somatic mutation rates in the progeny of flowering plants.

In humans, it is well known that the parental reproductive age has a strong influence on mutations transmitted to their progeny. Meiotic nondisjunction is known to increase in older mothers, and base substitutions tend to go up with paternal reproductive age. Hence, it is clear that the germinal mutation rates are a function of both maternal and paternal ages in humans.

Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation.

Seeds of flowering plants can be formed sexually or asexually through apomixis. Apomixis occurs in about 400 species and is of great interest for agriculture as it produces clonal offspring. It differs from sexual reproduction in three major aspects: (1) While the sexual megaspore mother cell (MMC) undergoes meiosis, the apomictic initial cell (AIC) omits or aborts meiosis (apomeiosis); (2) the unreduced egg cell of apomicts forms an embryo without fertilization (parthenogenesis); and (3) the formation of functional endosperm requires specific developmental adaptations.

Hybridization alters spontaneous mutation rates in a parent-of-origin-dependent fashion in Arabidopsis.

Over 70 years ago, increased spontaneous mutation rates were observed in Drosophila spp. hybrids, but the genetic basis of this phenomenon is not well understood. The model plant Arabidopsis (Arabidopsis thaliana) offers unique opportunities to study the types of mutations induced upon hybridization and the frequency of their occurrence.

Electronic transient spectroscopy from the deep UV to the NIR: unambiguous disentanglement of complex processes.

Complex multi-stage relaxation and reaction pathways after the optical excitation of molecules makes the disentanglement of the underlying mechanisms challenging. We present four examples that a new transient spectrometer with excitation fully tunable from the deep UV to the IR and 225 to 1700 nm probing allows for an analysis with greatly reduced ambiguity. The temporal resolution of about 50 fs allows us to resolve all relevant processes.

A comprehensive microscopic picture of the benzhydryl radical and cation photogeneration and interconversion through electron transfer.

Bond cleavage and bond formation are central to organic chemistry. Carbocations play a key role in our understanding of nucleophilic substitution reactions that involve both processes. The precise understanding of the mechanism and dynamics of the photogeneration of carbocations and carbon radicals is therefore an important quest.

SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing.

We present a generally applicable method allowing rapid identification of causal alleles in mutagenized genomes by next-generation sequencing. Currently used approaches rely on recovering homozygotes or extensive backcrossing. In contrast, SNP-ratio mapping allows rapid cloning of lethal and/or poorly transmitted mutations and second-site modifiers, which are often in complex genetic/transgenic backgrounds.

Photolytic generation of benzhydryl cations and radicals from quaternary phosphonium salts: how highly reactive carbocations survive their first nanoseconds.

UV irradiation (266 or 280 nm) of benzhydryl triarylphosphonium salts Ar(2)CH-PAr(3)(+)X(-) yields benzhydryl cations Ar(2)CH(+) and/or benzhydryl radicals Ar(2)CH(•). The efficiency and mechanism of the photo-cleavage were studied by nanosecond laser flash photolysis and by ultrafast spectroscopy with a state-of-the-art femtosecond transient spectrometer. The influences of the photo-electrofuge (Ar(2)CH(+)), the photo-nucleofuge (PPh(3) or P(p-Cl-C(6)H(4))(3)), the counterion (X(-) = BF(4)(-), SbF(6)(-), Cl(-), or Br(-)), and the solvent (CH(2)Cl(2) or CH(3)CN) were investigated.

Buildup and decay of the optical absorption in the ultrafast photo-generation and reaction of benzhydryl cations in solution.

The identification of the transition state or a short-lived intermediate of a chemical reaction is essential for the understanding of the mechanism. For a direct identification typically transient optical spectroscopy is used, preferentially with high temporal resolution. We combine broad-band femtosecond transient absorption measurements and on-the-fly molecular dynamics calculations to decipher the microscopic evolution of the geometry and solvation of photogenerated benzhydryl cations (Ar(2)CH(+), Ar = phenyl, p-tolyl, m-fluorophenyl, or m,m'-difluorophenyl) in bulk solution.

Genetic variation in healthy oldest-old.

Individuals who live to 85 and beyond without developing major age-related diseases may achieve this, in part, by lacking disease susceptibility factors, or by possessing resistance factors that enhance their ability to avoid disease and prolong lifespan. Healthy aging is a complex phenotype likely to be affected by both genetic and environmental factors. We sequenced 24 candidate healthy aging genes in DNA samples from 47 healthy individuals aged eighty-five years or older (the 'oldest-old'), to characterize genetic variation that is present in this exceptional group.