Compilation of tRNA sequences and sequences of tRNA genes.

Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA, is used. Sequences and references are available under http://www.uni-bayreuth. de/departments/biochemie/trna/     

Evolution of tRNA recognition systems and tRNA gene sequences

The aminoacylation of tRNAs by the aminoacyl-tRNA synthetases recapitulates the genetic code by dictating the association between amino acids and tRNA anticodons. The sequences of tRNAs were analyzed to investigate the nature of primordial recognition systems and to make inferences about the evolution of tRNA gene sequences and the evolution of the genetic code. Evidence is presented that primordial synthetases recognized acceptor stem nucleotides prior to the establishment of the three major phylogenetic lineages. However, acceptor stem sequences probably did not achieve a level of sequence diversity sufficient to faithfully specify the anticodon assignments of all 20 amino acids. This putative bottleneck in the evolution of the genetic code may have been alleviated by the advent of anticodon recognition. A phylogenetic analysis of tRNA gene sequences from the deep Archaea revealed groups that are united by sequence motifs which are located within a region of the tRNA that is involved in determining its tertiary structure. An association between the third anticodon nucleotide (N36) and these sequence motifs suggests that a tRNA-like structure existed close to the time that amino acid-anticodon assignments were being established. The sequence analysis also revealed that tRNA genes may evolve by anticodon mutations that recruit tRNAs from one isoaccepting group to another. Thus tRNA gene evolution may not always be monophyletic with respect to each isoaccepting group.Based on a presentation made at a workshop— Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code—held at Berkeley, CA, July 17–20, 1994 Correspondence to: M.E. Saks     

Molar and molecular views of choice

The molar and molecular views of behavior are not different theories or levels of analysis; they are different paradigms. The molecular paradigm views behavior as composed of discrete units (responses) occurring at moments in time and strung together in chains to make up complex performances. The discrete pieces are held together as a result of association by contiguity. The molecular view has a long history both in early thought about reflexes and in associationism, and, although it was helpful to getting a science of behavior started, it has outlived its usefulness. The molar view stems from a conviction that behavior is continuous, as argued by John Dewey, Gestalt psychologists, Karl Lashley, and others. The molar paradigm views behavior as inherently extended in time and composed of activities that have integrated parts. In the molar paradigm, activities vary in their scale of organization--i.e., as to whether they are local or extended--and behavior may be controlled sometimes by short-term relations and sometimes by long-term relations. Applied to choice, the molar paradigm rests on two simple principles: (a) all behavior constitutes choice; and (b) all activities take time. Equivalence between choice and behavior occurs because every situation contains more than one alternative activity. The principle that behavior takes time refers not simply to any notion of response duration, but to the necessity that identifying one action or another requires a sample extended in time. The molecular paradigm's momentary responses are inferred from extended samples in retrospect. In this sense, momentary responses constitute abstractions, whereas extended activities constitute concrete particulars. Explanations conceived within the molecular paradigm invariably involve hypothetical constructs, because they require causes to be contiguous with responses. Explanations conceived within the molar paradigm retain direct contact with observable variables.     

Molar scaling in strepsirrhine primates

We examined how maxillary molar dimensions change with body and skull size estimates among 54 species of living and subfossil strepsirrhine primates. Strepsirrhine maxillary molar areas tend to scale with negative allometry, or possibly isometry, relative to body mass. This observation supports several previous scaling analyses showing that primate molar areas scale at or slightly below geometric similarity relative to body mass. Strepsirrhine molar areas do not change relative to body mass(0.75), as predicted by the metabolic scaling hypothesis. Relative to basicranial length, maxillary molar areas tend to scale with positive allometry. Previous claims that primate molar areas scale with positive allometry relative to body mass appear to rest on the incorrect assumption that skull dimensions scale isometrically with body mass. We identified specific factors that help us to better understand these observed scaling patterns. Lorisiform and lemuriform maxillary molar scaling patterns did not differ significantly, suggesting that the two infraorders had little independent influence on strepsirrhine scaling patterns. Contrary to many previous studies of primate dental allometry, we found little evidence for significant differences in molar area scaling patterns among frugivorous, folivorous, and insectivorous groups. We were able to distinguish folivorous species from frugivorous and insectivorous taxa by comparing M1 lengths and widths. Folivores tend to have a mesiodistally elongated M1 for a given buccolingual M1 width when compared to the other two dietary groups. It has recently been shown that brain mass has a strong influence on primate dental eruption rates. We extended this comparison to relative maxillary molar sizes, but found that brain mass appears to have little influence on the size of strepsirrhine molars. Alternatively, we observed a strong correlation between the relative size of the facial skull and relative molar areas among strepsirrhines. We hypothesize that this association may be underlain by a partial sharing of the patterning of development between molar and facial skull elements.     

tRNA turnaround

Two recently published papers (Takano et al., 2005 and Shaheen and Hopper, 2005) demonstrate that in S. cerevisiae, cytoplasmic tRNAs can be transported into the nucleus. This retrograde movement may expose mature tRNAs to nuclear proofreading or it may regulate tRNA availability in response to amino acid availability.     

Light-induced absorbance changes of carotenoids in brown algae

Light-induced absorbance changes were studied for brown algae with 23 species and a pronounced absorbance change around 563 nm was found in all algae examined. 3-(3,4-dichlorophenyl)-1,1-dimethylurea and gramicidin J suppressed the initial rate and the magnitude of the absorbance change. Carbonylcyanidem-chlorophenylhydrazone did not affect the initial rate but decreased the maximum level of the change. All thalli and the chloroplasts tested had an absorption band at around 540 nm due to fucoxanthin which accounted for about 70–90% of the total carotenoids in brown algae. It is proposed that the 563 nm-change is caused by the red shift of fucoxanthin responding to the light-induced change in the membrane potential of the thylakoid system.     

Temperature-induced absorbance changes in developing barley chloroplasts

Absorbance changes on cooling and heating of barley ( Hordeum vulgare L. cv. IB65) chloroplasts greened for 12, 48 and 72 h were investigated to understand the structural changes during biogenesis of chloroplast membranes. Upon cooling the chloroplast suspension from 24 to 8°C, a positive absorbance change occurred at 678, 435 and 495 nm in 12, 48 and 72 h greened chloroplasts. During heating from 24 to 45°C negative absorbance changes were observed with some shifts in positions in different chloroplast preparations and a simultaneous increase in absorbance between 690 and 735 nm. For chloroplasts developed for 12, 48 and 72 h the changes in absorbance on cooling were 3.8, 3.3 and 1.9% at 678 nm, and on heating, 8.9, 8.3 and 4.1% at 680 nm.
The differences in absorbance changes are considered as an indication of variations in the structural organization and composition of developing chloroplasts. The reversibility of the absorbance changes was maximum in chloroplasts greened for 72 h and minimum in chloroplasts greened for 12 h. This would suggest that fully developed chloroplasts have more flexibility towards temperature-induced changes in the membranes.     

Dichroism of transient absorbance changes in the red spectral region using oriented chloroplasts. I. Field indicating absorbance changes

The light-induced transient absorbance changes which are affected by valinomycin have been studied using magnetically oriented spinach chloroplasts and a polarized measuring beam. The ΔA spectra for the two polarizations parallel and perpendicular to the plane of the photosynthetic membranes have been recorded in the spectral range 630–750 nm. Large polarization effects are found in all the bands of the ΔA spectrum, shifts in the position of the extrema are observed and the two spectra cross each other at various wavelengths. A comparison of these spectral features with available data on the dichroism of the Stark effect on monomolecular films of chlorophyll a and b indicates similarities favoring the already well documented hypothesis of the electrochromic nature of these absorbance changes in vivo.The data on this electrochromic effect can be correlated with the linear dichroism of oriented chloroplasts and the ΔA_∥?ΔA_⊥ spectrum in the 645–655 nm region gives further evidence of the orientation out of the membrane plane of the red transition moment of chlorophyll b.