DNA fingerprinting in clonal organisms

The use of DNA fingerprinting to identify members of the same clone in completely or partially asexual organisms requires that the individuals within a clone share a recent common ancestor. By considering the expected distributions of band–sharing values in asexual and sexual organisms, it is shown that DNA fingerprinting may be effective in distinguishing members of the same clone, provided that the frequency of sexual reproduction is considerably greater than the minisatellite mutation rate.     

Mitochondrial DNA,chloroplast DNA and the origins of development in eukaryotic organisms

Background  

Several proposals have been made to explain the rise of multicellular life forms. An internal environment can be created and controlled, germ cells can be protected in novel structures, and increased organismal size allows a "division of labor" among cell types. These proposals describe advantages of multicellular versus unicellular organisms at levels of organization at or above the individual cell. I focus on a subsequent phase of evolution, when multicellular organisms initiated the process of development that later became the more complex embryonic development found in animals and plants. The advantage here is realized at the level of the mitochondrion and chloroplast.     

Stabilizing synthetic data in the DNA of living organisms

Data-encoding synthetic DNA, inserted into the genome of a living organism, is thought to be more robust than the current media. Because the living genome is duplicated and copied into new generations, one of the merits of using DNA material is long-term data storage within heritable media. A disadvantage of this approach is that encoded data can be unexpectedly broken by mutation, deletion, and insertion of DNA, which occurs naturally during evolution and prolongation, or laboratory experiments. For this reason, several information theory-based approaches have been developed as an error check of broken DNA data in order to achieve data durability. These approaches cannot efficiently recover badly damaged data-encoding DNA. We recently developed a DNA data-storage approach based on the multiple sequence alignment method to achieve a high level of data durability. In this paper, we overview this technology and discuss strategies for optimal application of this approach.     

Doublet frequencies in the DNA of genetic code limit organisms

Summary Unrelated organisms with DNA of extreme G + C content (25% or 70%) are found to share very specific patterns of nearest neighbour base doublet frequency in their DNAs. This is shown to be a result of restrictions on the extremity of amino acid composition in their proteins, combined with a maximisation of the use of one type of base pair in redundant codon positions. Inferences are made about the universal nature of the genetic code and the proportion of DNA used for specifying protein in different species. The composition of coding DNA strands in these organisms is also discussed.     

Kinetic model of DNA replication in eukaryotic organisms

We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of different data within a simple theoretical framework. This allows one, for the first time, to determine the parameters governing the DNA replication program in a eukaryote on a genome-wide basis. In particular, we have determined the frequency of origin activation in time and space during the cell cycle. Although we focus on a specific stage of development, this model can easily be adapted to describe replication in many other organisms, including budding yeast.     

DNA probes in detection of spiroplasmas and mycoplasma-like organisms in plants and insects

Abstract DNA probes were applied to detect spiroplasmas and uncultivable mycoplasma-like organisms (MLOs) in infected plants and insects. The probes consisted of pMC5, a plasmid carrying the RNA genes of Mycoplasma capricolum and pRA1, a plasmid recovered from Spiroplasma citri . Southern blot hybridization of pMC5 with digested DNAs of periwinkle plants infected with S. citri , or with various MLOs, yielded 2 heavy and several weaker bands. The heavy hybridization bands were shown to represent rRNA genes of the plant chloroplasts, indicating significant nucleotide sequence homology between the mycoplasmal rRNA genes and those of plant chloroplasts. Some of the weaker hybridization bands, not revealed in DNA of healthy plants, appeared to represent rRNA gene sequences of the infectious agent. Use of the spiroplasma plasmid as a probe enabled the detection of S. citri in infected plant material and in hemolymph of infected leafhoppers at a high sensitivity level.     

Temperature adaptation of DNA ligases from psychrophilic organisms

DNA ligases operating at low temperatures have potential advantages for use in biotechnological applications. For this reason, we have characterized the temperature optima and thermal stabilities of three minimal Lig E-type ATP-dependent DNA ligase originating from Gram-negative obligate psychrophilic bacteria. The three ligases, denoted Vib-Lig, Psy-Lig, and Par-Lig, show a remarkable range of thermal stabilities and optima, with the first bearing all the hallmarks of a genuinely cold-adapted enzyme, while the latter two have activity and stability profiles more typical of mesophilic proteins. A comparative approach based on sequence comparison and homology modeling indicates that the cold-adapted features of Vib-Lig may be ascribed to differences in surface charge rather than increased local or global flexibility which is consistent with the contemporary emerging paradigm of the physical basis of cold adaptation of enzymes.

     

Related base sequences in the DNA of simple and complex organisms. I. DNA/DNA duplex formation and the incidence of partially related base sequences in DNA

A comparative study has been made of the reactions of bacteriophage T4, B. subtilis,and mouse DNA with homologous DNA trapped on a membrane filter. The variation of reaction rate with temperature provides information as to the number of unique and partially related base sequences. The thermal stability of the duplexes formed at various temperatures has been used as a criterion of the extent of base pairing. These studies suggest that no closely related base sequences exist within the T4 genome. Similar results were obtained with Bacillus subtilisDNA although the data suggest the possibility of some very distant intragenome homologies. In contrast, mouse DNA contains so many related base sequences that the predominant reaction product is always one containing partially complementary strands. These results suggest that gene duplication has been a major mechanism operative in the increase of DNA content of metazoans through evolution. The relationship between the existence of partial base sequence redundancies and the mechanism of recombination is also discussed. This research was supported by a grant from the National Science Foundation (GB 6099).     

Radiosensitivity of coding and noncoding DNA sequences of various organisms]

Relationship between pyrimidine distribution patterns and radiosensitivity (Z) of DNA molecules of different species was derived by computer analysis of recurrence frequency of pyrimidine clusters. Blocking factors (beta) and Z for coding and non-coding DNA sequences of species from different taxonomic classes have been calculated within a new model. The radiosensitivity of coding DNA sequences practically does not vary whereas Z values were increased during evolution from simplest to higher organisms. The beta and Z values calculated for several groups of individual genes were shown to vary considerably.     

DNA base composition of Microcyclus species and organisms of similar morphology

Summary From studies of the DNA base composition of Microcyclus species, it is concluded that the genus is to be regarded as a taxonomically heterogeneous group. This agrees with morphological observations of the different species.     

Random amplified polymorphic DNA analysis of genetically modified organisms

Randomly amplified polymorphic DNA (RAPD) was used to analyzed 78 samples comprises of certified reference materials (soya and maize powder), raw seeds (soybean and maize), processed food and animal feed. Combination assay of two arbitrary primers in the RAPD analysis enable to distinguish genetically modified organism (GMO) reference materials from the samples tested. Dendrogram analysis revealed 13 clusters at 45% similarity from the RAPD. RAPD analysis showed that the maize and soybean samples were clustered differently besides the GMO and non-GMO products.     

Potential effects of recombinant DNA organisms on ecosystems and their components

There are many examples of organisms which, by new genetic construction or by finding themselves in new habitats, have established large populations. Some have changed ecosystems drastically, some slightly, some apparently scarcely at all as a result. In the light of these natural and unintentional experiments, protocols for the examination of proposals for genetic release can be derived. The risk of damage will be small, but the damage that could be caused is large. Because of the variety and subtlety of ecological interactions, some dangerous organisms will be passed as safe. Methods of control need to be considered at the time of release.     

Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms

Topoisomerases are essential enzymes that solve topological problems arising from the double-helical structure of DNA. As a consequence, one should have naively expected to find homologous topoisomerases in all cellular organisms, dating back to their last common ancestor. However, as observed for other enzymes working with DNA, this is not the case. Phylogenomics analyses indicate that different sets of topoisomerases were present in the most recent common ancestors of each of the three cellular domains of life (some of them being common to two or three domains), whereas other topoisomerases families or subfamilies were acquired in a particular domain, or even a particular lineage, by horizontal gene transfers. Interestingly, two groups of viruses encode topoisomerases that are only distantly related to their cellular counterparts. To explain these observations, we suggest that topoisomerases originated in an ancestral virosphere, and that various subfamilies were later on transferred independently to different ancient cellular lineages. We also proposed that topoisomerases have played a critical role in the origin of modern genomes and in the emergence of the three cellular domains.     

Characteristics of nucleotide blocks in coding and non-coding DNA sequences from different organisms

A statistical analysis of occurrence of particular nucleotide runs (1 divided by 10 nucleotides long) in DNA sequences of different species has been carried out. There are considerable differences in run distributions in DNA sequences of prokaryotes, invertebrates and vertebrates. Distribution of various types of runs has been found to be different in coding and non-coding sequences. There is an abundance of short runs 1 divided by 2 nucleotides long in coding sequences, and there is a deficiency of such runs in the non-coding regions. However, some interesting exceptions from this rule exist: for run distribution of adenine in prokaryotes and for distribution of purine-pyrimidine runs in eukaryotes. This may be stipulated by the fact that the distribution of runs are predetermined by structural peculiarities of the entire DNA molecule. Runs of guanine or cytosine of three to six nucleotides long occur predominantly in the non-coding DNA regions in eukaryotes, especially in vertebrates.