No description available.

The thermophilic enzyme, Thermus aquaticus (Taq) DNA polymerase, is an essential tool in molecular biology because of its ability to synthesis DNA in vitro and its inherent thermal stability. Taq DNA polymerase is widely used in the polymerase chain reaction (PCR), an essential technique in a broad range of different fields from academic research to clinical diagnostics. The use of PCR-based tests in diagnostic testing is ever increasing; however, many of the samples being tested contain substances that inhibit PCR and prevent target amplification. Many attempts have been made to engineer polymerases not only to increase resistance to overcome the problem of inhibition, but also to enhance other characteristics such as fidelity, processivity and thermostability. Heparin, found in blood samples, and phytate, found in faecal samples, are two examples from a number of known PCR inhibitors. The mode of action of most PCR inhibitors is not well understood, but inhibition is thought to occur by enzyme binding or through the chelation of Mg2+ ions essential for PCR. In this project, a system of directed evolution by compartmentalised self-replication (CSR) was established and successfully employed to screen a mutant library for Taq DNA polymerase variants with enhanced resistance to the inhibitors heparin and phytate. CSR is a recently-established high-throughput method for the creation of novel polymerases, based on a feedback loop whereby polymerase variants replicate their own encoding gene. A mutant library of 106 variants was produced by random mutagenesis error-prone PCR, in which only the polymerase domain of Taq was mutagenised. Firstly, the CSR system was established and tested by performing a screen in the presence of heparin to select for heparin-resistant variants. Characterisation of selected variants revealed that a single round of CSR had produced a Taq variant (P550S, T588S) with a 4-fold increase in heparin resistance. The IC50 was increased from 0.012U/ml heparin to 0.050U/ml heparin. The study with heparin was followed by a phytate screen, in which two rounds of CSR were performed with an initial round of error-prone PCR followed by re-diversification (recombination) of the mutant library using the staggered extension process (StEP). The two rounds of CSR yielded a Taq variant with a 2-fold increase in phytate-resistance compared to the wild-type, with IC50 increased from 360μM phytate to 700μM phytate. The best phytate mutant (P685S, M761V, A814T) was further characterised and it was found that the catalytic activity, thermostability and fidelity of the mutant were comparable to the wildtype enzyme. The position of resistance-conferring mutations of the novel Taq variants evolved in this study provided some evidence for the inhibitors’ predicted modes of action in the case 2 of both phytate and heparin. As phytate’s mode of action is poorly understood, further investigations were performed to elucidate its role in PCR inhibition. A thorough investigation into the importance of relative phytate and Mg2+ levels on PCR was conducted and revealed for the first time convincing evidence that the primary mode of phytatemediated PCR inhibition is by chelation. Further work led to the successful crystallisation of Taq in the presence of phytate, although subsequent X-ray diffraction data to 2.5Å did not reveal phytate bound within the enzyme structure. Site-directed mutagenesis studies were used to probe cross-over between heparin and phytate-conferring mutations. Thus, in addition to providing valuable information for novel Taq variants with a potential application in fecal-based PCR diagnostic tests, this project has begun to provide insight into the fundamental aspects of the mode of action of phytate as a polymerase and PCR inhibitor.

In previous publications [1,7] the author described the base rivalry in monotonous DNA sequences and their effect on the DNA repair mechanism. According to this theory, many base building blocks compete for the occupancy of the newly released base site in the replication of monotonous DNA sequences in the elongation phase. This gives them more and more kinetic energy from replication position k to next position. Thus, there is a probability that a tautomeric base pair is formed behind the end of the monotonic sequence because of the tunneling effect. After its replication a different, irreparable base pair develops from the tautomeric base pair, when the rivalry - energy leads to a very strong hydrogen bond. This happens, however, by chance. In the following, we will describe the 3 phenomena: The tunnel probability (section 2), the probability for coming up of a high – energy – base building block (Elitist, section 3),and the combination of both phenomena (section 4). The result of these calculations is the equation (28). It is remarkable that follows from these calculations that the length of the monotonous sequences, and also the length of DNA increases itself in the course of evolution (section 5). (Read up all detailed computations in [7].) [... from introduction]

No description available.

During the cell division dynamic processes take place, the origin of which are to find in the physical characteristics of cell components. The most important characteristics are the electrical charge and the energy of the moving base components in a viscous cytoplasm. During the emergence of the new hydrogen bonds takes place a competition of the complementary base components which are electrostatically attracted by the codogen matrix. Thus, the base components will be accelerated more and more in the course of replication, and the resulting binding energies become always larger in a monotonous sequence. We call this process “base rivalry”. It is shown that the strength of these new bindings depends on three factors: First it is dependent on the length of a monotonous sequence, second it is dependent on the viscosity of the cytoplasm, and third it is dependent on the replication speed. In the study in detail is stated, how it affects the effectiveness of the DNA repair mechanism, mutation susceptibility, and thus also affects the cancer susceptibility. This is a condition where the DNA repair mechanism fails: Because of the base rivalry, in a monotonous base sequence there is (for a short time) a high binding energy between the complementary bases from a critical sequence length upwards, and the effectiveness of the repair mechanism is strongly decreased. If a tautomeric base pair is behind the end of monotonous sequence, then an extension of the monotonous sequence is provoked so that, for example, the monotonous sequence CCCT irreparably changes itself into CCCC (see section 2.2). The author describes in detail how the base rivalry affects on the evolution and on the mutation of viruses. The probability for the emergence of an irreparable mutation (caused by base rivalry) will be calculated. The result is (for a large number of individuals) a mathematical connection between temperature and the length of monotonous DNA - sequences which are lengthened by base rivalry. In the study, there are preferentially used physical and statistical computations and therefore is to understand as theoretical work. For the examination of this theory, two different computations are necessary: 1. Statistical computation: It is safe to assume that an individual base component exists (for example, dGTP) having a very large fading time in the case of excitation (preferable, owing to rotation energy after it became lumpy). Such a base component is very rarely, so that it appears within a DNA-fragment either not or once at most. This is called the “elitist”. If it appears within the fragment, we can compute the probability for its appearance in a certain position during replication, namely in a monotonous sequence of this fragment. The calculation of the probability must be statistically, because the replication is a distribution on the codogen matrix. 2. Physical computation: If the elitist (accidentially) arrives at a monotonous sequence of the DNA-fragment, it will reach the end of this monotonous sequence because of its high base rivalry energy, and now we can the tunnel probability calculate for the conversion into the tautomeric form which leads to a mutated hydrogen Bond at the end of monotonous sequence. This mutated hydrogen bond is irreparabel, if the fading time of the excited elitist higher is than the repair time of the DNA repair mechanism. Both probabilities have to be connected for the computation of the total probability of the irreparable mutation. The result of this connection is an interesting equation between temperature and monotonous sequence length which is irreparably lengthened, and this gives rise to the speculation that this theory as well as the resulting equation may have a certain importance for the theory of evolution, and may have an importance for the dangerous virus mutations. If several base rivalries take place in a monotonous sequence of a DNA fragment over time and with decreasing cell temperature, an extension of the fragment and thus a DNA extension is provoked at each base rivalry (section 8.1). In the appendix [28] are supplementary remarks in order to understand the sections better. There is, too, a remark concerning the coherence between tumor development and cell - viscosity.

In previous publications [1,7] the author described the base rivalry in monotonous DNA sequences and their effect on the DNA repair mechanism. According to this theory, many base building blocks compete for the occupancy of the newly released base site in the replication of monotonous DNA sequences in the elongation phase. This gives them more and more kinetic energy from replication position to next position. Thus, there is a probability that a tautomeric base pair is formed behind the end of the monotonic sequence because of the tunneling effect. After its replication a different, irreparable base pair develops from the tautomeric base pair, when the rivalry - energy leads to a very strong hydrogen bond. This happens, however, by chance. In the following, we will describe the 3 phenomena: The tunnel probability (section 2), the probability for coming up of a high – energy – base building block (Elitist, section 3),and the combination of both phenomena (section 4). The result of these calculations is the equation (28). It is remarkable that follows from these calculations that the length of the monotonous sequences, and also the length of DNA increases itself in the course of evolution (section 5). (Read up all detailed computations in [7].) [... from introduction]

Hox genes code for transcription factors that play a major role in the development of all animal phyla. In invertebrates these genes usually occur as tightly linked cluster, with a few exceptions where the clusters have been dissolved. Only in vertebrates multiple clusters have been demonstrated which arose by duplication from a single ancestral cluster. This history of Hox cluster duplications, in particular during the early elaboration of the vertebrate body plan, is still poorly understood. In this paper we report the results of a PCR survey on genomic DNA of the pacific hagfish Eptatretus stoutii. Hagfishes are one of two clades of recent jawless fishes that are an offshoot of the early radiation of jawless vertebrates. Our data provide evidence for at least 33 distinct Hox genes in the hagfish genome, which is most compatible with the hypothesis of multiple Hox clusters. The largest number, seven, of distinct homeobox fragments could be assigned to paralog group 9, which could imply that the hagfish has more than four clusters. Quartet mapping reveals that within each paralog group the hagfish sequences are statistically more closely related to gnathostome Hox genes than with either amphioxus or lamprey genes. These results support two assumptions about the history of Hox genes: (1) The association of hagfish homeobox sequences with gnathostome sequences suggests that at least one Hox cluster duplication event happened in the stem of vertebrates, i.e., prior to the most recent common ancestor of jawed and jawless vertebrates. (2) The high number of paralog group 9 sequences in hagfish and the phylogenetic position of hagfish suggests that the hagfish lineage underwent additional independent Hox cluster/-gene duplication events.

The phylogenetic position of Xenoturbella bocki has been a matter of controversy since its description in 1949. We sequenced a second complete mitochondrial genome of this species and performed phylogenetic analyses based on the amino acid sequences of all 13 mitochondrial protein-coding genes and on its gene order. Our results confirm the deuterostome relationship of Xenoturbella. However, in contrast to a recently published study (Bourlat et al. in Nature 444:85–88, 2006), our data analysis suggests a more basal branching of Xenoturbella within the deuterostomes, rather than a sister-group relationship to the Ambulacraria (Hemichordata and Echinodermata).

DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as D. melanogaster and C. elegans. In this thesis we report on a comprehensive study of the pres- ence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. We observe that loss of individual DNMTs independently occured multiple times across ecdysozoan phyla. In several cases, this resulted in a loss of DNA methylation. In vertebrates, however, there is no single species known which lost DNA methylation. Actually, DNA methylation was greatly expanded after the 1R/2R whole genome duplication (WGD) and became a genome-wide phe- nomena. In our study of vertebrates we are not looking for losses of DNA methyltransferases and DNA methylation but are rather interested in the gain of additional DNA methyltransferase genes. In vertebrates there were a number of WGD. Most vertebrates only underwent two WGD but in the teleost lineage a third round of WGD occured and in some groups, e.g. Salmoniformes and some Cypriniformes even a forth WGD occured. The Carp-specific WGD (4R) is one of the most recent vertebrate WGD and is estimated to have occured 12.4 mya. We performed the most comprehen- sive analysis of the evolution of DNA methyltransferases after vertebrate whole-genome duplications (WGD) so far. We were able to show that the conservation of duplicated DNMT3 genes in Salmoniformes is more diverse than previously believed. We were also able to identify DNA methyltrans- ferases in Cypriniformes which have, due to their recent WGD, quite com- plex genomes. Our results show that the patterns of retained and lost DNA methyltransferases after a forth round of WGD differ between Cypriniformes and Salmoniformes. We also proposed a new nomenclature for teleost DNMT genes which correctly represents the orthology of DNMT genes for all teleost species. Next to these purely computational projects we collaborated with the Aluru lab to investigate the effects of different disturbances on zebrafish DNA methylation. One disturbance is the inactivation of DNMT3aa and DNMT3ab as single knockouts as well as a double knockout. This was the first double knockout of DNMT genes in zebrafish which was ever generated. It allows us to study the subfunctionalization of the two DNMT3a genes their effect on genome-wide DNA methylation. Given our results we hypothesize that DNMT3aa and DNMT3ab can compensate for each other to a high de- gree. DNMT3a genes have likely been subfuntionalized but their loss can be compensated by DNMT3b genes. This compensation by DNMT3b genes works well enough that no notable phenotype can be observed in double knockout zebrafish but a difference is notable on the epigenome level. The second disturbance we studied is the exposure of zebrafish to the toxic chemi- cal PCB126. We detected a moderate level of DNA methylation changes and a much larger effect on gene expression. Similar to previous reports we find little correlation between DNA methylation and gene expression changes. Therefore, while PCB126 exposure has a negative effect on DNA methyla- tion it is likely that other gene regulatory mechanisms play a role as well, possibly even a greater one. How do genes evolve and how are genes regulated are two of the main questions of modern molecular biology. In this thesis we have tried to shed more light on both questions. we have broadly expanded the phylogenetic range of species with a manually curated set of DNA methyltransferases. We have done this for ecdysozoan species which have lost all DNA methylating enzymes as well as for teleost fish which acquired more than ten copies of the, originally, two genes. We were also able to generate new insight into the subfunctionalization of the DNA methylation machinery in zebrafish and how it reacts to environmental effects.:1 Introduction 1.1 Biological introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.2 Detecting DNA methylation . . . . . . . . . . . . . . . . . . . . . . . . 7 2 Evolution of DNA methylation across Ecdysozoa 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 2.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 3 Evolution of DNA methyltransferases after vertebrate whole genome duplications 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 3.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 4 The effect of DNMT3aa and DNMT3ab knockout on DNA methyla- tion in zebrafish 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 4.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 4.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 4.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 5 Role of DNA methylation in altered testis gene expression patterns in adult zebrafish exposed to Pentachlorobiphenyl 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 5.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 5.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 5.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 6 Conclusions 6.1 Evolution of DNA methylation across Ecdysozoa . . . . . . . . . . . . . 95 6.2 Evolution of DNA methyltransferases after vertebrate whole genome duplications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 6.3 Role of DNA methylation in altered testis gene expression patterns in adult zebrafish (Danio rerio) exposed to Pentachlorobiphenyl (PCB 126). . . 107 6.4 Knockout of DNMT3aa and DNMT3ab in zebrafish (Danio rerio) . . . . . . 108 Bibliography 119

In a process called 'base rivalry', irreparable mutations are provoked in the replication of monotonous sequences, which depend on the cell temperature, the cell viscosity and monotonous sequence length. This explains the very long monotonous sequences and very long DNAs that occur over long evolutionary epochs. Presumably, base rivalry (with tautomerism or too low cell viscosity) also provokes the formation of tumors and the emergence of dangerous viral mutations.