Kenji Sorimachi

A Proposed Solution to the Historic Puzzle of Chargaff's Second Parity Rule

Chargaff s first parity rule for the contents of the four nucleotides in DNA is easily understood based on the double-stranded DNA structure. However, the second parity rule, based on similar nucleotide relationships in single- stranded DNA, has been a puzzle in molecular biology, because it is impossible to imagine how pairs of G and C, and A and T are formed in the single DNA strand. In the present study, Chargaffs second parity rule can be solved based on nu- cleotide contents and the correlation between the two strands in double-stranded DNA.

Inhibitory Effect of Agaricu blazei Murill Components on Abnormal Collagen Fiber Formation in Human Hepatocarcinoma Cells

Hot-water extracts of the mycelial culture and fruiting bodies of Agaricus blazei Murill were fractionated by ethanol precipitation, using various ethanol concentrations. The mycelial fraction (A-4) inhibited abnormal collagen fiber formation, and fractions A-1 to A-3 showed a small inhibitory effect. The strongest inhibition was obtained by fraction A-4, and no significant inhibition was observed with fractions A-5 and A-6. With the fruiting bodies, fractions B-1 to B-6 showed no inhibitory effects on collagen fiber formation in HCC. The reverse transcription-polymerase chain reaction (RT-PCR) demonstrates that Agaricus blazei mycelial fraction A-4 did not inhibit the type I, II or III procollagen gene expression.

The most primitive extant ancestor of organisms and discovery of definitive evolutionary equations

Organisms are classified into three domains, Prokaryota, Archaea, and Eukaryota, and their evolutionary divergence has been characterized based on morphological and molecular features using rationale based on Darwin’s theory of natural selection. However, universal rules that govern genome evolution have not been identified. Here, a simple, innovative approach has been developed to evaluate biological evolution initiating the origin of life: whole genomes were divided into several fragments, and then differences in normalized nucleotide content between nucleotide pairs were compared. Based on nucleotide content structures, Monosiga brevicollis mitochondria may be the most primitive extant ancestor of the species examined here. The two normalized nucleotide contents are universally expressed by a linear regression line, (X − Y)/(X + Y) = a (X − Y) + b, where X and Y are nucleotide contents and (a) and (b) are constants. The value of (G + C), (G + A), (G + T), (C + A), (C + T) and (A + T) was ~0.5. Plotting (X − Y)/(X + Y) against X/Y showed a logarithmic function (X − Y)/(X + Y) = a ln X/Y + b, where (a) and (b) are constant. Nucleotide content changes are expressed by a definitive equation, (X − Y) ≈ 0.25 ln(X/Y).

The Most Primitive Extant Ancestor of Organisms and Discovery of Definitive Evolutionary Equations Based on Complete Genome Structures

Evolutionary divergence has been characterized based on morphological and molecular features using rationale based on Darwin’s theory of natural selection. However, universal rules that govern genome evolution have not been identified. Here, a simple, innovative approach has been developed to evaluate biological evolution initiating the origin of life: whole genomes were divided into several fragments, and then differences in normalized nucleotide content between nucleotide pairs were compared. Intramolecular nucleotide differences in complete mitochondrial genomes reflect evolutionary divergence. The values of (G – C), (G – T), (G – A), (C – T), (C – A) and (T – A) reflect biological evolution, and these values except for (G – C) and (T – A) change inversely to positive from negative along biological evolution of bacterial genomes. More highly evolved organisms, such as primates and birds, seem to have greater levels of (C – T) in mitochondria. Based on nucleotide content structures, Monosiga brevicollis mitochondria may be the most primitive extant ancestor of the species examined here. The two normalized nucleotide contents are universally expressed by a linear regression line, (X – Y)/(X + Y) = a(X – Y) + b, where X and Y are nucleotide contents and (a) and (b) are constants. The value of (G + C), (G + A), (G + T), (C + A), (C + T) and (A + T) was ~0.5. Plotting (X – Y)/(X + Y) against X/Y showed a logarithmic function (X – Y)/(X + Y) = a lnX/Y + b, where (a) and (b) are constant. Nucleotide content changes are expressed by a definitive equation, (X – Y) ≈ 0.25 ln(X/Y).