Directional mutation pressure,mutator mutations,and dynamics of molecular evolution

Using a general form of the directional mutation theory, this paper analyzes the effect of mutations in mutator genes on the G + C content of DNA, the frequency of substitution mutations, and evolutionary changes (cumulative mutations) under various degrees of selective constraints. Directional mutation theory predicts that when the mutational bias between A/T and G/C nucleotide pairs is equilibrated with the base composition of a neutral set of DNA nucleotides, the mutation frequency per gene will be much lower than the frequency immediately after the mutator mutation takes place. This prediction explains the wide variation of the DNA G + C content among unicellular organisms and possibly also the wide intragenomic heterogeneity of third codon positions for the genes of multicellular eukaryotes. The present analyses lead to several predictions that are not consistent with a number of the frequently held assumptions in the field of molecular evolution, including belief in a constant rate of evolution, symmetric branching of phylogenetic trees, the generality of higher mutation frequency for neutral sets of nucleotides, the notion that mutator mutations are generally deleterious because of their high mutation rates, and teleological explanations of DNA base composition. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992     

Metabolism and Translocation of Gibberellins in the Seedlings of Pharbitis nil (II). Photoperiodic Effects on Metabolism and Translocation of Gibberellins Applied to Cotyledons

We investigated the metabolism and translocation of two gibberellins(GAs), [³H]GA₂₀ and [³H]GA₁, which were applied at low concentrationto the cotyledons of Pharbitis nil (cv. Violet). Seedlings weregrown under three different photoperiodic conditions: continuouslight (CL-CL), continous light followed by short day conditions(CL-DT) and long day conditions followed by short day conditions(DT-DT). Translocation of the applied [³H]GAs from cotyledonsto hypocotyls was promoted by DT for all GAs examined. Whilethe conversion of the translocated [³H]GA₁ to [³H]GA₈ and itsconjugates was rapid in hypocotyl, the conversion of translocated[³H]GA₂₀ to [³H]GA₂₉ was slow. Radioactivity in epicotyls wasdetected much more rapidly on application of [³H]GA₂₀ than of[³H]GA₁, [³H]GA₈ and [³H]GA₂₉ and their conjugates. The conversionof [³H]GA₂₀ to [³H]GA₁ in the epicotyl was more rapid underCL-CL conditions. This result in consistent with the higherlevel of endogenous GA₁ existing in epicotyls under CL-DT thanDT-DT conditions. However, when [³H]GA₁ was applied to the cotyledon,only small amounts of [³H]GA₈ and its conjugates were detectedin the epicotyl regardless of the photoperiodic conditions.This result may suggest that the translocation and metabolismof [³H]GA₂₀ from cotyledons to epicotyl was faster under CL-CLthan DT-DT conditions and may correlate with the increased epicotylelongation of GA₂₀ treated plants under CL-DT than DT-DT conditions. (Received June 28, 1995; Accepted November 2, 1995)     

Radioadaptive response: Efficient repair of radiation-induced DNA damage in adapted cells

To verify the hypothesis that the induction of a novel, efficient repair mechanism for chromosomal DNA breaks may be involved in the radioadaptive response, the repair kinetics of DNA damage has been studied in cultured Chinese hamster V79 cells with single-cell gel electrophoresis. The cells were adapted by priming exposure with 5 cGy of γ-rays and 4-h incubation at 37°C. There were no indication of any difference in the initial yields of DNA double-strand breaks induced by challenging doses from non-adapted cells and from adapted cells. The rejoining of DNA double-strand breaks was monitored over 120 min after the adapted cells were challenged with 5 or 1.5 Gy, doses at the same level to those used in the cytogenetical adaptive response. The rate of DNA damage repair in adapted cells was higher than that in non-adapted cells, and the residual damage was less in adapted cells than in non-adapted cells. These results indicate that the radioadaptive response may result from the induction of a novel, efficient DNA repair mechanism which leads to less residual damage, but not from the induction of protective functions that reduce the initial DNA damage.     

Amino acid intrinsic alpha-helical propensities III: positional dependence at several positions of C terminus

In this study, we have analyzed experimentally the helical intrinsic propensities of non-charged and non-aromatic residues at different C-terminal positions (C1, C2, C3) of an Ala-based peptide. The effect was found to be complex, resulting in extra stabilization or destabilization, depending on guest amino acid and position under consideration. Polar (Ser, Thr, Cys, Asn, and Gln) amino acids and Gly were found to have significantly larger helical propensities at several C-terminal positions compared with the alpha-helix center (-1.0 kcal/mole in some cases). Some of the nonpolar residues, especially beta-branched ones (Val and Ile) are significantly more favorable at position C3 (-0.3 to -0.4 kcal/mole), although having minor differences at other C-terminal positions compared with the alpha-helix center. Leu has moderate (-0.1 to -0.2 kcal/mole) stabilization effects at position C2 and C3, whereas being relatively neutral at C1. Finally, Met was found to be unfavorable at C1 and C2 ( +0.2 kcal/mole) and favorable at C3 (-0.2 kcal/mole). Thus, significant differences found between the intrinsic helical propensities at the C-terminal positions and those in the alpha-helix center must be accounted for in helix/coil transition theories and in protein design.     

Significance of rooting depth in mire plants: Evidence from natural <Superscript>15</Superscript>N abundance

Variation in stable nitrogen isotope ratios (¹⁵N) was assessed for plants comprising two wetland communities, a bog-fen system and a flood plain, in central Japan. ¹⁵N of 12 species from the bog-fen system and six species from the flood plain were remarkably variable, ranging from –5.9 to +1.1 and from +3.1 to +8.7, respectively. Phragmites australis exhibited the highest ¹⁵N value at both sites. Rooting depth also differed greatly with plant species, ranging from 5cm to over 200cm in the bog-fen system. There was a tendency for plants having deeper root systems to exhibit higher ¹⁵N values; plant ¹⁵N was positively associated with rooting depth. Moreover, an increasing gradient of peat ¹⁵N was found along with depth. This evidence, together with the fact that inorganic nitrogen was depleted under a deep-rooted Phragmites australis stand, strongly suggests that deep-rooted plants actually absorb nitrogen from the deep peat layer. Thus, we successfully demonstrated the diverse traits of nitrogen nutrition among mire plants using stable isotope analysis. The ecological significance of deep rooting in mire plants is that it enables those plants to monopolize nutrients in deep substratum layers. This advantage should compensate for any consequential structural and/or physiological costs. Good evidence of the benefits of deep rooting is provided by the fact that Phragmites australis dominates as a tall mire grass.     

Clinical Course and Changes in High-Resolution Computed Tomography Findings in Patients with Idiopathic Pulmonary Fibrosis without Honeycombing

Some patients with idiopathic pulmonary fibrosis (IPF) do not have honeycombing on high-resolution computed tomography (HRCT) at their initial evaluation. The clinical course and sequential changes in HRCT findings in these patients are not fully understood. We reviewed the cases of 43 patients with IPF without honeycombing on initial HRCT from institutions throughout Japan. All patients were diagnosed with IPF based on a surgical lung biopsy. Multidisciplinary discussions were held five times between 2011 and 2014, to exclude alternative etiologies. We evaluated the sequential changes in HRCT findings in 30 patients with IPF. We classified these 30 patients into three groups based on their HRCT patterns and clarified the clinical characteristics and prognosis among the groups. The patterns of all 30 patients on initial HRCT corresponded to a possible usual interstitial pneumonia (UIP) pattern which was described in the 2011 International Statement. On long-term follow-up (71.0±38.7 standard deviation [SD] months), honeycombing was seen in 16 patients (53%, the HoneyCo group); traction bronchiectasis or cysts without honeycombing was observed in 12 patients (40%, the NoHoneyCo group), and two patients showed no interval change (7%, the NoChange group) on HRCT. The mean survival periods of the HoneyCo and NoHoneyCo groups were 67.1 and 61.2 months, respectively (p = 0.76). There are some patients with IPF whose conditions chronically progress without honeycombing on HRCT. The appearance of honeycombing on HRCT during the follow-up might not be related to prognosis.     

Structural Basis for the Dual Substrate Specificity of DOCK7 Guanine Nucleotide Exchange Factor

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Reduced Renal α-Klotho Expression in CKD Patients and Its Effect on Renal Phosphate Handling and Vitamin D Metabolism

Renal α-Klotho (α-KL) plays a fundamental role as a co-receptor for fibroblast growth factor 23 (FGF23), a phosphaturic hormone and regulator of 1,25(OH)₂ vitamin D₃ (1,25VitD₃). Disruption of FGF23-α-KL signaling is thought to be an early hallmark of chronic kidney disease (CKD) involving reduced renal α-KL expression and a reciprocal rise in serum FGF23. It remains unclear, however, whether the rise in FGF23 is related to the loss of renal α-KL. We evaluated α-KL expression in renal biopsy samples and measured levels of several parameters of mineral metabolism, as well as soluble α-KL (sKL), in serum and urinary samples from CKD patients (n = 236). We found that although renal α-KL levels were significantly reduced and serum FGF23 levels were significantly elevated in early and intermediate CKD, serum phosphate levels remained within the normal range. Multiple regression analysis showed that the increases in FGF23 were significantly associated with reduced renal function and elevated serum phosphate, but were not associated with loss of renal α-KL. Moreover, despite falling renal α-KL levels, the increase in FGF23 enhanced urinary fractional excretion of phosphate and reduced serum 1,25VitD₃ levels in early and intermediate CKD, though not in advanced CKD. Serum sKL levels also fell significantly over the course of CKD, and renal α-KL was a significant independent determinant of sKL. These results demonstrate that FGF23 levels rise to compensate for renal failure-related phosphate retention in early and intermediate CKD. This enables FGF23-α-KL signaling and a neutral phosphate balance to be maintained despite the reduction in α-KL. In advanced CKD, however, renal α-KL declines further. This disrupts FGF23 signaling, and serum phosphate levels significantly increase, stimulating greater FGF23 secretion. Our results also suggest the serum sKL concentration may be a useful marker of renal α-KL expression levels.     

A kinetic mechanism for the fast movement of Chara myosin

Endoplasmic streaming of characean cells of Nitella or Chara is known to be in the range 30-100 microm/second. The Chara myosin extracted from the cells and fixed onto a glass surface was found to move muscle actin filaments at a velocity of 60 microm/second. This is ten times faster than that of skeletal muscle myosin (myosin II). In this study, the displacement caused by single Chara myosin molecules was measured using optical trapping nanometry. The step size of Chara myosin was approximately 19nm. This step size is longer than that of skeletal muscle myosin but shorter than that of myosin V. The dwell time of the steps was relatively long, and this most likely resulted from two rate-limiting steps, the dissociation of ADP and the binding of ATP. The rate of ADP release from Chara myosin after the completion of the force-generation step was similar to that of myosin V, but was considerably slower than that of skeletal muscle myosin. The 19nm step size and the dwell time obtained could not explain the fast movement. The fast movement could be explained by the load-dependent release of ADP. As the load imposed on the myosin decreased, the rate of ADP release increased. We propose that the interaction of Chara myosin with an actin filament resulted in a negative load being imposed on other myosin molecules interacting with the same actin filament. This resulted in an accelerated release of ADP and the fast sliding movement.