A B S T R A C T Title: Recombination of Ions in Plasma at 50 − 300 K Author: Peter Rubovič Supervisor: Prof. RNDr. Juraj Glosík, DrSc. Abstract: Main part of this doctoral thesis lies in a study of recom- bination of atomic and molecular ions in low temperature plasmatic environment with emphasis on effect of third bodies. Stationary After- glow equipped with Cavity Ring Down Spectrometer and Cryogenic Flowing Afterglow with Langmuir Probe II were used to obtain recom- bination rate coefficients. Electron assisted collisional radiative recom- bination of Ar+ ion was studied in the temperature range of 50−100 K and helium assisted collisional radiative recombination was observed too. Both H+ 3 and its isotopologue D+ 3 were studies in flowing after- glow and spectroscopically in stationary afterglow as well. Binary re- combination rate coefficients and ternary recombination rate coeffi- cients for helium assisted ternary recombination were determined in the temperature range of 50 − 250 K. These coefficients were deter- mined also for pure ortho- and para- nuclear spin configurations of H+ 3 in the temperature range of 80 − 200 K. Keywords: dissociative recombination, collisional radiative recombi- nation, H+ 3 , D+ 3 , Ar+ viii

The concept of species in bacteria is a matter of contention. The current definition is based on DNA-DNA hybridisation and does not account for evolutionary forces that are important in demarcating species. In this thesis we investigate two evolutionary forces that are important in speciation in bacteria, propose novel statistical models for them and infer parameters of interest. We present the first attempt at inferring the bias in the recombination process from whole bacterial genomes. Despite empirical evidence that recombination is biased and theoretical results that this bias is important in speciation, it is usually ignored. We propose a coalescent based model that accounts for the bias in the recombination process. We use approximate Bayesian computation for inference and describe an efficient method for simulating from the model. We show that our method performs well on simulated datasets and is robust to slight misspecification of the history of the samples. Application of our method to a Bacillus cereus dataset shows that it contain evidence that the recombination process depends on the evolutionary distance between donors and recipients. We demonstrate that the rate of bias in the recombination process for this dataset is far lower than what theoretical studies require for the spontaneous generation of populations that can be called species under neutral model. Next we propose a model for occurrence of adaptive events on a phylogenetic tree. We use the model to infer the boundaries of clusters on a phylogenetic tree that correspond to ecologically distinct lineages. we characterise our method using simulated datasets and show that it is conservative in estimating the number of adaptive events. Finally we apply our method to two bacterial datasets of Salmonella enterica and Vibrionaceae. We show that there is decisive evidence that isolates in these datasets partition into numerous ecologically distinct lineages and use our method to delineate the boundaries of these lineages.

Meiotic recombination is a fundamental biological process in sexually reproducing organisms, enabling offspring to inherit novel combinations of mutations, and ensuring even segregation of chromosomes into gametes. Recombination is initiated by programmed Double Strand Breaks (DSBs), the genomic locations of which are determined in most mammals by PRDM9, a rapidly evolving DNA-binding protein. In crosses between different mouse subspecies, certain Prdm9 alleles cause infertility in hybrid males, implying a critical role in fertility and speciation. Upon binding to DNA, PRDM9 deposits a histone modification (H3K4me3) typically found in the promoters of expressed genes, suggesting that binding might alter the expression of nearby genes. Many other questions have remained about how PRDM9 initiates recombination, how it causes speciation, and why it evolves so rapidly. This body of work investigates these questions using complementary experimental and analytical methodologies. By generating a map of human PRDM9 binding sites and applying novel sequence analysis methods, I uncovered new DNA-binding modalities of PRDM9 and identified sequence-independent factors that predict binding and recombination outcomes. I also confirmed that PRDM9 can affect gene expression by binding to promoters, identifying candidate regulatory targets in meiosis. Furthermore, I showed that PRDM9’s DNA-binding domain also mediates strong protein-protein interactions that produce PRDM9 multimers, which may play an important functional role. Finally, by generating high-resolution maps of PRDM9 binding in hybrid mice, I provide evidence for a mechanism to explain PRDM9-mediated speciation as a consequence of the joint evolution of PRDM9 and its binding targets. This work reveals that PRDM9 binding on one chromosome strongly impacts DSB formation and/or repair on the homologue, suggesting a novel role for PRDM9 in promoting efficient homology search and DSB repair, both critical for meiotic progression and fertility. One consequence is that PRDM9 may play a wider role in mammalian speciation.

Commonly, when it is desirable to replace an essential gene with an allelic series of mutated genes, or genes with altered expression patterns, the complementing constructs are introduced into heterozygous plants, followed by the selection of homozygous null segregants. To overcome this laborious and time-consuming step, the newly developed two-component system utilizes a site-specific recombinase to excise a wild-type copy of the gene of interest from transformed tissues. In the first component (the first vector), a wild-type version of the gene is placed between target sequences recognized by FLP recombinase from the yeast 2 μm plasmid. This construct is transformed into a plant heterozygous for a null mutation at the endogenous locus, and progeny plants carrying the excisable complementing gene and segregating homozygous knockout at the endogenous locus are selected. The second component (the second vector) carries the experimental gene along with the FLP gene. When this construct is introduced, FLP recombinase excises the complementing gene, leaving the experimental gene as the only functional copy. The FLP gene is driven by an egg apparatus specific enhancer (EASE) to ensure excision of the complementing cDNA in the egg cell and zygote following floral-dip transformation. The utility of this system is being tested using various experimental derivatives of the essential sucrose-proton symporter, AtSUC2, which is required for photoassimilate transport.

Homologous recombination (HR) and nonhomologous end joining (NHEJ) are two distinct DNA double-stranded break (DSB) repair pathways. Here, we report that DNA-dependent protein kinase (DNA-PK), the core component of NHEJ, partnering with DNA-damage checkpoint kinases ataxia telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR), regulates HR repair of DSBs. The regulation was accomplished through modulation of the p53 and replication protein A (RPA) interaction. We show that upon DNA damage, p53 and RPA were freed from a p53-RPA complex by simultaneous phosphorylations of RPA at the N-terminus of RPA32 subunit by DNA-PK and of p53 at Ser37 and Ser46 in a Chk1/Chk2-independent manner by ATR and ATM, respectively. Neither the phosphorylation of RPA nor of p53 alone could dissociate p53 and RPA. Furthermore, disruption of the release significantly compromised HR repair of DSBs. Our results reveal a mechanism for the crosstalk between HR repair and NHEJ through the co-regulation of p53-RPA interaction by DNA-PK, ATM and ATR.

Homologous recombination (HR) and nonhomologous end joining (NHEJ) are two distinct DNA double-stranded break (DSB) repair pathways. Here, we report that DNA-dependent protein kinase (DNA-PK), the core component of NHEJ, partnering with DNA-damage checkpoint kinases ataxia telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR), regulates HR repair of DSBs. The regulation was accomplished through modulation of the p53 and replication protein A (RPA) interaction. We show that upon DNA damage, p53 and RPA were freed from a p53-RPA complex by simultaneous phosphorylations of RPA at the N-terminus of RPA32 subunit by DNA-PK and of p53 at Ser37 and Ser46 in a Chk1/Chk2-independent manner by ATR and ATM, respectively. Neither the phosphorylation of RPA nor of p53 alone could dissociate p53 and RPA. Furthermore, disruption of the release significantly compromised HR repair of DSBs. Our results reveal a mechanism for the crosstalk between HR repair and NHEJ through the co-regulation of p53-RPA interaction by DNA-PK, ATM and ATR.

In this master thesis, electrical characterization of thin film CuInxGa(1−x)Se2 solar cells produced by Midsummer AB were performed with the aim of determining the dominant recombination path of these cells. Current-Voltage (IV), Quantum Effinciency (QE), temperature dependent IV (IVT) and Drive-Level Capacitance Profiling (DLCP) was used with the objective to investigate the dominant recombination path as well as provide some insight of the solar cells in order to create a baseline model using the modelling software SCAPS (Solar cell CAPacitance Simulator). The IV produced mostly consistent results with slight variation, most likely due to non uniformity of equipment. The QE showed consistent results between all cells indicating a stable process for the sample preparation. Using IVT measurements were taken from a temperature of 115K −300K in order to obtain the activation energy for the dominant recombination path. By comparing it with the band gap energy from the QE measurement, it was found that the dominant recombination path is in either the space charge region or in the bulk of the CIGS and not at the hetero interface. DLCP measurement were made at both low temperature and at room temperature and revealed that the cells had a similar doping as other comparable cells at 7×1016cm−3 . The initial baseline model created in SCAPS show a good agreement with the measured IV and currently indicates a spike in the band alignment, supporting the results for the IVT measurement.

The understanding of basic cellular processes has been greatly facilitated through investigation of the behaviour of mutant forms. In a similar way the mechanisms of genetic recombination may be clarified by a study of strains which are known to show inherited differences in recombination behaviour at meiosis. The haploid fungus Neurospora crassa is particularly well suited to such an investigation since recombination frequency heterogeneity has been extensively reported in that organism, and the differences are believed to be, to a large extent, under genetic control. Strains showing recombination frequency heterogeneity over a marked genetic region have been extensively analysed in the present work and the mode of action of the factors controlling recombination frequency has been investigated by combining differing strains in heterokaryons. / Thesis / Doctor of Philosophy (PhD)

La recombinaison génétique est un processus biologique fondamental, ayant lieu au cours de la méiose et assurant la bonne ségrégation des chromosomes, ainsi que le maintien de la variabilité génétique grâce au brassage intrachromosomique. La recombinaison a été étudiée dans de nombreuses espèces, en particulier chez les Mammifères et les animaux d’élevage, comme les bovins, les porcs ou les ovins. Dans tous les cas, une variation du taux de recombinaison a été observée entre les individus et il a été démontré qu’elle était héritable et sous déterminisme génétique. Dans certaines espèces, des cartes génétiques ont également été construites, ce qui a permis de localiser les crossingovers et de détecter de très petites zones du génome où la recombinaison était importante : les points chauds. En race ovine Lacaune, de nombreuses données de génotypages sont disponibles, notamment grâce à l’existence de deux puces : une de moyenne densité avec 54 000 marqueurs et une de haute densité avec 600 000 marqueurs. Deux jeux de données étaient donc disponibles ; un jeu de données familial avec près de 6 000 individus apparentés et génotypés pour les 54 000 marqueurs et un jeu de données comportant 70 Lacaune non apparentés et génotypés pour les 600 000 marqueurs. Des cartes génétiques ont donc été créées pour ces deux jeux de données. Avec les animaux non apparentés, environ 50 000 points chauds ont été détectés. Le jeu de données familial a permis d’observer des motifs de distribution de la recombinaison communs aux autres Mammifères. Enfin, la combinaison des deux jeux de données a révélé la présence de signatures de sélection et a permis de créer une carte génétique de haute densité. De plus, une variation du taux de recombinaison a été observée entre les individus et a pu être liée à l’existence de 2 QTLs majeurs sur les chromosomes 6 et 7. Des gènes candidats plus ou moins bien connus ont pu être proposés, voire étudiés : RNF212 et HEI10. De plus, une comparaison avec une autre population ovine a permis de montrer que les cartes de recombinaison étaient quasiment identiques, mais que le taux de recombinaison individuel était soumis à un déterminisme génétique différent. Il a également été possible de proposer une application concrète pour l’utilisation des cartes génétiques en sélection génomique, grâce à la création de puces basse densité pouvant être utilisées pour l’imputation des reproducteurs et donc favoriser le génotypage et la sélection génomique à moindre coût. / Genetic recombination is a fundamental biological process, which occurs during the meiosis. It allows the good segregation of the chromosomes and contributes to maintain the genetic diversity. Recombination was already studied in a lot of different species, especially in mammals and in farm animals, such as the pig, the cattle or the sheep. In each case, a variation of the recombination rate between the individuals was observed. This variation was heritable and under genetic determinism. In some species, genetic recombination maps were also created, which allowed to localize the crossovers and to detect really tiny genomic regions where the recombination is huge: the recombination hotspots. In the Lacaune breed sheep, a lot of genotyping data are available thanks to two existing arrays: a first with a medium density of markers (about 54,000 markers) and a second with a high density of markers (about 600,000 markers). Two datasets were thus available: a familial dataset with about 6,000 animals genotyped for the 54,000 markers and a dataset of 70 unrelated Lacaune genotyped for the 600,000 markers. Genetic recombination maps were created for these two datasets. With the 70 unrelated Lacaune, about 50,000 hotspots were detected. The familial dataset allowed to observe the mammals common recombination patterns. Finally, when the two datasets were combined, selection signatures were revealed and a high density recombination map were created. Furthermore, a variation of the recombination rate within the individuals was observed and was associated to 2 main QTLs on the chromosomes 6 and 7. Already known, or not, candidate genes were proposed and sometimes studied: especially RNF212 and HEI10. Finally, a comparison with another sheep breed revealed that the genetic recombination maps were really similar, but the individual recombination rate was under a different genetic determinism. A concrete application of the genetic recombination map in genomic selection was also proposed thanks to the creation of lowdensity SNPs sets, which could be used to impute the animals and thus to improve the genotyping and the genomic selection for lessercosts.

Meiotic recombination involves the exchange of DNA between two homologous chromosomes, forming cross-overs and gene conversion events. The cross-over process is important for the proper segregation of chromosomes during meiosis, and drives genetic diversity. Human hotspots are enriched for a 13-bp motif, CCNCCNTNNCCNC; a close match to this motif occurs in about 40% of our cross-over hotspots. A DNA binding protein called PRDM9, having histone trimethyltransferase (H3K4me3) activity, binds the motif and is becoming established as a major determinant of recombination hotspots (narrow regions with high cross-over activity). This research aimed to understand the mechanisms involved in promoting PRDM9 binding to its target sites, and subsequently, initiating cross-over hotspot activity. We first explored the relationship between PRDM9 binding and DNA sequence, to directly confirm whether PRDM9 binds to the 13-bp hotspot motif using in-vitro gel-shift assays, and found that it does bind sequence specifically to the canonical 13-mer motif. PRDM9 is able to bind the motif in a highly selective manner, with certain single base pair changes abolishing binding. However, we observe that it is also able to tolerate degeneracy in its binding sites, as demonstrated by strong in-vitro binding to degenerate versions of the 13-bp motif. Hence, these results confirmed that PRDM9 is able to directly bind to the 13-bp hotspot motifs, and given that it can also tolerate degeneracy, this raised the question of why PRDM9 is able to bind only a subset of all such potential binding sites in the genome. To address this, a ChIP-seq analysis was performed to identify genome wide binding sites for PRDM9. This information also helped us to characterise binding sites and investigate if factors such as the local chromatin environment play a role in specifying PRDM9 binding tar- gets and hotspot formation. We were able to identify over 170,000 PRDM9 binding sites in the genome. Surprisingly, these binding sites were also enriched in promoter regions, however, bound sites in these regulatory regions showed low recombination activity. We found that PRDM9 is able to confer the H3K4me3 mark on all bound sites, even those without a pre-existing H3K4me2 mark. We also investigated the role of other chromatin related marks on PRDM9 binding and found that binding occurs in chromatin accessible, but nucleosome rich regions, whereas heterochromatin regions tend to inhibit binding. Further, for hotspot formation, it was seen that less chromatin accessible, nucleosome dense regions away from transcribed sites, are preferred. Hotspots tend to avoid regions marked by transcription activating histone modifications, however, these regions do not appear to inhibit PRDM9 binding itself. These results show how PRDM9 binding in the genome is dependent on both primary DNA sequence and the surrounding epigenetic factors. Together these factors promote binding and, with additional downstream factors, positioning of hotspot locations in the human genome.