The three classes of triplet profiles of natural genomes

AbstractBased on the huge variety of different genomes, one may expect a correspondingly large variety of the frequency distribution of their trinucleotides (“triplet profiles”). Yet, this article reports the unexpected finding that there are essentially only three kinds of triplet profiles among the large number of genomes examined here. None of the classes included random profiles, all of them contained members from vastly different taxa and species. Since the three classes of genomes do not reflect the phylogeny of their member organisms, I propose that these classes may reflect species-independent mechanisms of genome evolution

The Motile Behavior of Virus-Transformed 3T3 Cells

Using metallic gold in various assays for the motility of cultured tissue cells, the paper compares the movements of surface projections and the locomotion of polyoma (Py3T3) and SV40 (SV3T3) virus-transformed 3T3 cells with the behavior of the parental 3T3 cells. The movement of surface projections was assayed by the ability of filopodia, lamellipodia and blebs of freshly plated cells to remove colloidal gold particles from a particle-coated glass substrate. The ability of filopodia to probe the environment for points of anchoraqe was tested by observing cells plated on glass whose filopodia touched the surface of a neighboring area of evaporated gold. The locomotion of cells was assayed by particle-free tracks (phagokinetic tracks) which were left by migrating cells on a glass substrate which was previously coated with colloidal gold particles. The paper suggests that the ability of the transformed cells to sense environmental factors, and their behavioral controls are altered

Outline of a Genome Navigation System Based on the Properties of GA-Sequences and Their Flanks

Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments. Although not integral parts of them, Alu-elements were found immediately upstream of all human and chimpanzee GA-sequences with an upstream poly(A)-segment. The article hypothesizes that genome navigation uses these properties of GA-sequences in the following way. (1) Poly(A) binding proteins interact with the upstream poly(A)-segments and arrange adjacent GA-sequences side-by-side (‘GA-ribbon’), while folding the intervening DNA sequences between them into loops (‘associated DNA-loops’). (2) Genome navigation uses the GA-ribbon as a search path for specific target genes that is up to 730-fold shorter than the full-length chromosome. (3) As to the specificity of the search, each molecule of a target protein is assumed to catalyze the formation of specific oligomers from a set of transcription factors that recognize tetra-GA-motifs. Their specific combinations of tetra-GA motifs are assumed to be present in the particular GA-sequence whose associated loop contains the gene for the target protein. As long as the target protein is abundant in the cell it produces sufficient numbers of such oligomers which bind to their specific GA-sequences and, thereby, inhibit locally the transcription of the target protein in the associated loop. However, if the amount of target protein drops below a certain threshold, the resultant reduction of specific oligomers leaves the corresponding GA-sequence ‘denuded’. In response, the associated DNA-loop releases its nucleosomes and allows transcription of the target protein to proceed. (4) The Alu-transcripts may help control the general background of protein synthesis proportional to the number of transcriptionally active associated loops, especially in stressed cells. (5) The model offers a new mechanism of co-regulation of protein synthesis based on the shared segments of different GA-sequences

Properties and Distribution of Pure GA-Sequences of Mammalian Genomes

The article describes DNA sequences of mammalian genomes that are longer than 50 bases, but consist exclusively of G’s and A’s (‘pure GA-sequences’). Although their frequency of incidence should be 10 216 or smaller, the chromosomes of human, chimpanzee, dog, cat, rat, and mouse contained many tens of thousands of them ubiquitously located along the chromosomes with a species-dependent density, reaching sizes of up to 1300 [b]. With the exception of a small number of poly-A-, poly-G-, poly-GA-, and poly-GAAA-sequences (combined,0.5%), all pure GA-sequences of the mammals tested were unique individuals, contained several repeated short GA-containing motifs, and shared a common hexa-nucleotide spectrum. At most 2 % of the human GA-sequences were transcribed into mRNAs; all others were not coding for proteins. Although this could have made them less subject to natural selection, they contained 160 times fewer point mutations than one should expect from the genome at large. As to the presence of other sequences with similarly restricted base contents, there were approximately as many pure TC-sequences as pure GA-sequences, but many fewer pure AC-, TA, and TGsequences. There were practically no pure GC-sequences. The functions of pure GA-sequences are not known. Supported by a number of observations related to heat shock phenomena, the article speculates that they serve as genomic sign posts which may help guide polymerases and transcription factors to their proper targets, and/or as spatial linkers that hel

Guenter Albrecht-Buehler to John Philip Trinkaus, January 27, 1976

Letter to Trinkaus inviting him to give a seminar at Cold Spring Harbor Laboratory in March 1976.Typed letter; includes some handwritten notes at the bottom of page1-pageCorrespondenc