The Impact of Message Mutation on the Fitness of a Genetic Code

The Standard Genetic Code is organized such that similar codons encode similar amino acids. One explanation suggested that the Standard Code is the result of natural selection to reduce the fitness ``load' that derives from the mutation and mistranslation of protein-coding genes. We review the arguments against the mutational load-minimizing hypothesis and argue that they need to be reassessed. We review recent analyses of the organization of the Standard Code and conclude that under cautious interpretation they support the mutational load-minimizing hypothesis. We then present a deterministic asexual model with which we study the mode of selection for load minimization. In this model, individual fitness is determined by a protein phenotype resulting from the translation of a mutable set of protein-coding genes. We show that an equilibrium fitness may be associated with a population with the same genetic code and that genetic codes that assign similar codons to similar amino acids have a higher fitness. We also show that the number of mutant codons in each individual at equilibrium, which determines the strength of selection for load minimization, reflects a long-term evolutionary balance between mutations in messages and selection on proteins, rather than the number of mutations that occur in a single generation, as has been assumed by previous authors. We thereby establish that selection for mutational load minimization acts at the level of an individual in a single generation. We conclude with comments on the shortcomings and advantages of load minimization over other hypotheses for the origin of the Standard Code. Received: 4 April 2001 / Accepted: 22 October 2001     

Optimisation or satiation,testing diet selection rules in goats

Several hypotheses have been formulated to explain diet selection by herbivores, focusing on the maximization of nutrient intake, the minimization of plant secondary compounds, or the satiety hypothesis. This research aimed at studying diet selection revealing which chemical characteristics of plants form the bases for dietary preferences of goats. This was done by setting up a feeding experiment with three different combinations of tree species Acacia karroo, A. nilotica and A. sieberana. The chemical characteristics of these three Acacia species were used to predict diet selection. To test the validity of the satiety hypothesis, goats were placed on a conditioning diet of one of the three species. We found a clear preference for A. karroo and an avoidance of A. nilotica when these two were offered to the goats. In trials where A. nilotica was present, tannin minimization was the best explaining diet selection rule. In trials where A. nilotica was not present, however, tannin minimization was not the best explanation. Our findings suggest that tannins are not avoided but kept below a certain threshold. Below this threshold, goats based their dietary choices on other chemical characteristics of the Acacia species. Acid detergent fibre (ADF) minimization could then best explain preferences in trials with Acacia karroo and A. sieberana that have generally low tannin content. Goats did not maximize nutrient intake or digestibility, and we found no support for the satiety hypothesis.     

Total work rate of breathing optimization in CO-2 inhalation and exercise.

The hypothesis that respiratory frequency and the relative durations of inspiration and expiration are regulated according to a total cycle work rate minimization criterion was explored. Effects of negative work performed by the respiratory muscles and dead space variation as a function of tidal volume were included in a formulation which yielded a theoretically predictable optimal frequency and relative duration of inspiration and expiration at all levels of ventilation. Predicted cycle characteristics based on measured mechanical parameters were compared with data taken during CO-2 inhalation (3 and 5%) and moderate exercise (MRR = 3 and 6) in three normal human subjects. No major difference in breathing pattern was observed between CO-2 inhalation and exercise. Results suggest that conditions for minimization of total cycle work rate are achieved asympototically as the level of ventilation rises above the resting level. At rest and at low levels of hyperpnea complete work rate optimization is not achieved.     

Information processing limits on generating neuroanatomy: global optimization of rat olfactory cortex and amygdala

A pattern of widespread connection optimization in the nervous system has become evident: deployment of some neural interconnections attains optimality, sometimes without detectable limits. New results for optimization of layout of connected areas of rat olfactory cortex and of rat amygdala are reported here. One larger question concerns mechanisms—how such minimization is attained. A next question is why a nervous system would optimize rather than just moderately satisfice. A morphogenic proposal that relates these questions is that the means of organizing neural wiring happens also to yield optimization. Some neuroanatomy is generated via “saving wire,” and this optimizing is via simple physical processes rather than DNA-mediated mechanisms. Such “non-genomic nativism” is thereby a path around fundamental limitations on generating brains, some of the most complex structures in the known universe.     

Guidelines to come to minimized tensile strength loss upon cellulase application

Application of cellulase technology in the textile production process often results in a certain loss of tensile strength along with the desired performance. In this paper guidelines are given how to come to minimization or even prevention of tensile strength loss. Part of the considerations is based on the hypothesis given in the accompanying paper (Lenting and Warmoeskerken, 2001, J. Biotechnol.) concerning the mechanism of interaction between cellulase action and applied shear force. Recommendations given concern the enzyme choice, process parameters and enzyme targeting.     

Characterization by NMR and molecular modeling of the binding of polyisoprenols and polyisoprenyl recognition sequence peptides: 3D structure of the complexes reveals sites of specific interactions

The objective of these studies was to test the hypothesis that proteins that contain potential polyisoprenyl recognition sequences (PIRSs) in their transmembrane-spanning domain can bind to the polyisoprenyl (PI) glycosyl carrier lipids undecaprenyl phosphate (C55-P) and dolichyl phosphate (C95-P). A number of prokaryotic and eukaryotic glycosyltransferases that utilize PI coenzymes contain a conserved PIRS postulated to be the active PI binding domain. To study this problem, we first determined the 3D structure of a PIRS peptide, NeuE, by homonuclear 2D 1H-nuclear magnetic resonance (NMR) spectroscopy. Experimentally generated distance constraints derived from nuclear Overhauser enhancement and torsion angle constraints derived from coupling constants were used for restrained molecular dynamics and energy minimization calculations. Molecular models of the NeuE peptide were built based on calculations of energy minimization using the DGII program NMRchitect. 3D models of dolichol (C95) and C95-P were built based on our 2D 1H-NMR nuclear Overhauser enhancement spectroscopy (NOESY) results and refined by energy minimization with respect to all atoms using the AMBER (assisted modeling with energy refinements) force field. Our energy minimization studies were carried out on a conformational model of dolichol that was originally derived from small-angle X-ray scattering and molecular mechanics methods. These results revealed that the PIs are conformationally nearly identical tripartite molecules, with their three domains arranged in a coiled, helical structure. Analyses of the intermolecular cross-peaks in the 2D NOESY spectra of PIRS peptides in the presence of PIs confirmed a highly specific interaction and identified key contact amino acids in the NeuE peptide that constituted a binding motif for interacting with the PIs. These studies also showed that subtle conformational changes occurred within both the PIs and the NeuE peptide after binding. 3D structures of the resulting molecular complexes revealed that each PI could bind more than one PIRS peptide. These studies thus represent the first evidence for a direct physical interaction between specific contact amino acids in the PIRS peptides and the PIs and supports the hypothesis of a bifunctional role for the PIs. The central idea is that these superlipids may serve as a structural scaffold to organize and stabilize in functional domains PIRS-containing proteins within multiglycosyltransferase complexes that participate in biosynthetic and translocation processes.     

Novel and efficient RNA secondary structure prediction using hierarchical folding.

Algorithms for prediction of RNA secondary structure-the set of base pairs that form when an RNA molecule folds-are valuable to biologists who aim to understand RNA structure and function. Improving the accuracy and efficiency of prediction methods is an ongoing challenge, particularly for pseudoknotted secondary structures, in which base pairs overlap. This challenge is biologically important, since pseudoknotted structures play essential roles in functions of many RNA molecules, such as splicing and ribosomal frameshifting. State-of-the-art methods, which are based on free energy minimization, have high run-time complexity (typically Theta(n(5)) or worse), and can handle (minimize over) only limited types of pseudoknotted structures. We propose a new approach for prediction of pseudoknotted structures, motivated by the hypothesis that RNA structures fold hierarchically, with pseudoknot-free (non-overlapping) base pairs forming first, and pseudoknots forming later so as to minimize energy relative to the folded pseudoknot-free structure. Our HFold algorithm uses two-phase energy minimization to predict hierarchically formed secondary structures in O(n(3)) time, matching the complexity of the best algorithms for pseudoknot-free secondary structure prediction via energy minimization. Our algorithm can handle a wide range of biological structures, including kissing hairpins and nested kissing hairpins, which have previously required Theta(n(6)) time.     

Waveform characterization of the soybean stem feeder Edessa meditabunda: overcoming the challenge of wiring pentatomids for EPG

Stink bugs (Hemiptera: Heteroptera: Pentatomidae) are in general robust and restless insects, which makes them difficult to wire for electropenetrograph (EPG) studies. In addition, cuticular lipids may reduce wire effectiveness, and their removal could improve success of wiring. We compared wiring effectiveness for three species of stink bugs, differing in walking behaviour and degree of cuticular waxiness, that is, Piezodorus guildinii (Westwood), Nezara viridula (L.), and Loxa deducta (Walker). Results indicated that removal of cuticular lipids by mechanical abrasion (via sanding) greatly improved attachment success with gold wire. Our hypothesis that heavier and bigger bugs would lose the wire attachment more quickly than lighter and smaller bugs was not confirmed, regardless of the sanding. In contrast, our hypothesis that greater movement of a bug would cause the wire to break more often was supported by extensive testing. Behaviour appears to be more relevant for successful wiring than body weight. We used the sanding and wiring technique to characterize and correlate direct current EPG waveforms for the large and restless stem‐feeding stink bug Edessa meditabunda (Fabricius) on soybean plants. This marks the first published example of pentatomid EPG waveforms. Edessa meditabunda recordings on soybean stems generated eight types of waveforms in three phases and two families, named as follows: non‐probing = Np and Z; pathway phase = Em1; X wave phase = X; ingestion phase, family I = Em2 and Em3; ingestion phase, family N = Em4 and Em5. These eight were described based on their frequencies, relative amplitudes, and level voltages. Histological studies of stylets within salivary sheaths correlated the Em1, Em2, and Em3 waveforms with specific penetration sites. The waveform with the longest duration when feeding was Em2, representing xylem sap ingestion; in addition, waveform Em3 (always preceded by an X wave) was correlated with phloem sap ingestion.     

MOL3D,a modular and interactive program for molecular modeling and conformational analysis: I — basic modules

MOL3D is a generalized machine-independent computer program that lets the user interactively build 3D structures with different display options, such as wire, ball-and-stick and CPK representations. The program, which uses its own graphics package and driver, is designed to be very user friendly through the use of commands and menus. It has powerful transformation capabilities, such as software rotations, superpositions and zooming, and it is equipped with a fragment database that allows the user to build complex structures. The algorithm presented here is designed to perform computations in all the conformational space and therefore can be used to predict experimentally available quantities, such as NMR coupling constants. The program is efficient in the sense that it handles only dihedral angles in the first steps; as a result, it allows a rapid sampling of a great number of points through the entire conformational space. The user can choose between grid and Monte-Carlo searches of energy minimization, using a reasonable amount of computer time.     

Blood-seeking horseflies prefer vessel-imitating temperature gradients on host-mimicking targets: Experimental corroboration of a new explanation of the visual unattractiveness of zebras to tabanids

Several hypotheses tried to explain the advantages of zebra stripes. According to the most recent explanation, since the borderlines of sunlit white and black stripes can hamper thermal vessel detection by blood-seeking female horseflies, striped host animals are unattractive to these parasites which prefer hosts with a homogeneous coat, on which the temperature gradients above blood vessels can be detected more easily. This hypothesis has been tested in a field experiment with horseflies walking on a grey barrel with thin black stripes which were slightly warmer than their grey surroundings in sunshine, while in shade both areas had practically the same temperature. To eliminate the multiple (optical and thermal) cues of this test target, we repeated this experiment with improved test surfaces: we attracted horseflies by water- or host-imitating homogeneous black test surfaces, beneath which a heatable wire ran. When heated, this invisible and mechanically impalpable wire imitated thermally the slightly warmer subsurface blood vessels, otherwise it was thermally imperceptible. We measured the times spent by landed and walking horseflies on the test surface parts with and without underlying heated or unheated wire. We found that walking female and male horseflies had no preference for any (wired or wireless) area of the water-imitating horizontal plane test surface on the ground, independent of the temperature (heated or unheated) of the underlying wire. These horseflies looked for water, rather than a host. On the other hand, in the case of host-imitating test surfaces, female horseflies preferred the thin surface regions above the wire only if it was heated and thus warmer than its surroundings. This behaviour can be explained exclusively with the higher temperature of the wire given the lack of other sensorial cues. Our results prove the thermal vessel recognition of female horseflies and support the idea that sunlit zebra stripes impede the thermal detection of a host‘s vessels by blood-seeking horseflies, the consequence of which is the visual (non-thermal) unattractiveness of zebras to horseflies.     

Residential magnetic fields predicted from wiring configurations: II. Relationships To childhood leukemia.

Case-control data on childhood leukemia in Los Angeles County were reanalyzed with residential magnetic fields predicted from the wiring configurations of nearby transmission and distribution lines. As described in a companion paper, the 24-h means of the magnetic field's magnitude in subjects' homes were predicted by a physically based regression model that had been fitted to 24-h measurements and wiring data. In addition, magnetic field exposures were adjusted for the most likely form of exposure assessment errors: classic errors for the 24-h measurements and Berkson errors for the predictions from wire configurations. Although the measured fields had no association with childhood leukemia (P for trend=.88), the risks were significant for predicted magnetic fields above 1.25 mG (odds ratio=2.00, 95% confidence interval=1.03-3.89), and a significant dose-response was seen (P for trend=.02). When exposures were determined by a combination of predictions and measurements that corrects for errors, the odds ratio (odd ratio=2.19, 95% confidence interval=1.12-4.31) and the trend (p =.007) showed somewhat greater significance. These findings support the hypothesis that magnetic fields from electrical lines are causally related to childhood leukemia but that this association has been inconsistent among epidemiologic studies due to different types of exposure assessment error. In these data, the leukemia risks from a child's residential magnetic field exposure appears to be better assessed by wire configurations than by 24-h area measurements. However, the predicted fields only partially account for the effect of the Wertheimer-Leeper wire code in a multivariate analysis and do not completely explain why these wire codes have been so often associated with childhood leukemia. The most plausible explanation for our findings is that the causal factor is another magnetic field exposure metric correlated to both wire code and the field's time-averaged magnitude.     

Unexpectedly enhanced stereoselectivity of peroxidase-catalyzed sulfoxidation in branched alcohols

Lyophilized horseradish peroxidase (HRP) exhibits poor stereoselectivity in the sulfoxidation of thioanisole when the enzyme is either redissolved in water or suspended in organic solvents. However, when HRP is co-lyophilized in the presence of lyoprotectants or ligands, its stereoselectivity, although still low in most organic solvents, increases up to 4-fold if assayed in secondary or tertiary alcohols (but not in their linear isomers). A mechanistic hypothesis is presented explaining this puzzling phenomenon on the basis of a model of the active site of the enzyme-substrate complex derived from its X-ray crystal structure by means of molecular dynamics and energy minimization.     

The economy of the shape of limbed animals

A simple, high-level wire-minimization model appears to drive the relationship between animal limb number and body-to-limb proportion in some animals across at least seven phyla: annelids, arthropods, cnidarians, echinoderms, molluscs, tardigrades and vertebrates. Given an animal's body-to-limb proportion, the model enables one to estimate the animal's number of limbs, and vice versa. Informally, the model states that a limbed animal's large-scale morphology is set so as to maximize its number of limbs subject to the constraint that there is not a more economical shape which reaches out to the same places. A consequence of animals conforming to the model is that their large-scale morphology is “minimally wired.” Just as wire minimization is important in artificial information processing devices, it is hypothesized that one reason why animals' large-scale morphologies conform to a save-wire principle is to minimize the system-wide information processing times. Received: 10 November 1999 / Accepted in revised form: 9 June 2000     

Study of high- and low-current-configuration homes from the 1988 Denver Childhood Cancer Study

An epidemiological study conducted by Savitz et al. reported that residential wire codes were more strongly associated with childhood cancer than were measured magnetic fields, a peculiar result because wire codes were originally developed to be a surrogate for residential magnetic fields. The primary purpose of the study reported here, known as the Back to Denver (BTD) study, was to obtain data to help in the interpretation of the original results of Savitz et al. The BTD study included 81 homes that had been occupied by case and control subjects of Savitz et al., stratified by wire code as follows: 18 high current configuration (HCC) case homes; 20 HCC control homes; 20 low current configuration (LCC) case homes; and 23 LCC control homes. Analysis of new data acquired in these homes led to the following previously unpublished conclusions. The home-averaged (i.e., mean of fields measured in subjects' bedrooms, family/living rooms, and rooms where meals normally eaten) spot 60 Hz, 180 Hz, and harmonic (i.e., 60-420 Hz) magnetic fields were associated with wire codes. The 180 Hz and harmonic components, but not the 60 Hz component, were associated with case/control status. Measured static magnetic fields were only weakly correlated (rapproximately 0.2) between rooms in homes. The BTD data provide little support for, but are too sparse to definitively test, the 1995 resonance hypothesis proposed by Bowman et al. Case and control homes had similar concentrations of copper in their tap water. Copper concentration was not associated with wire codes nor with the level of electric current carried by a home's water pipe. These results of the BTD study suggest that future case/control studies investigating power frequency magnetic fields might wish to include measurements of 180 Hz or harmonic magnetic fields in order to examine their associations (if any) with disease status.     

A Mechanochemical Model for Embryonic Pattern Formation: Coupling Tissue Mechanics and Morphogen Expression

Motivated by recent experimental findings, we propose a novel mechanism of embryonic pattern formation based on coupling of tissue curvature with diffusive signaling by a chemical factor. We derive a new mathematical model using energy minimization approach and show that the model generates a variety of morphogen and curvature patterns agreeing with experimentally observed structures. The mechanism proposed transcends the classical Turing concept which requires interactions between two morphogens with a significantly different diffusivity. Our studies show how biomechanical forces may replace the elusive long-range inhibitor and lead to formation of stable spatially heterogeneous structures without existence of chemical prepatterns. We propose new experimental approaches to decisively test our central hypothesis that tissue curvature and morphogen expression are coupled in a positive feedback loop.     

Variation in the effect of profitability on prey size selection by the lacertid lizard Psammodromus algirus

Maximizing the average rate of energy intake (profitability) may not always be the optimal foraging strategy for ectotherms with relatively low energy requirements. To test this hypothesis, we studied the feeding behaviour of captive insectivorous lizards Psammodromus algirus, and we obtained experimental estimates of prey mass, handling time, profitability, and attack distance for several types of prey. Handling time increased linearly with prey mass and differed significantly among prey types when prey size differences were controlled for, and mean profitabilities differed among prey taxa, but profitability was independent of prey size. The attack distance increased with prey length and with the mobility of prey, but it was unrelated to profitability. Thus, lizards did not seem to take account of the rate of energy intake per second as a proximate cue eliciting predatory behavior. This information was combined with pitfall-trap censuses of prey (in late April, mid-June and late July) that allowed us to compare the mass of the prey captured in the environment with that of the arthropods found in the stomachs of sacrificed free-living lizards. In April, when food abundance was low and lizards were reproducing, profitability had a pronounced effect on size selection and lizards selected prey larger than average from all taxa except the least profitable ones. As the active season progressed, and with a higher availability of food, the number of prey per stomach decreased and their mean ize increased. The effect of profitability on size selection decreased (June) and eventually vanished (July–August). This variation is probably related to seasonal changes in the ecology of lizards, e.g. time minimization in the breeding season as a means of saving time for nonforaging activities versus movement minimization by selecting fewer (but larger) prey in the postbreeding season. Thus, the hypothesis that maximizing profitability could be just an optional strategy for a terrestrial ectothermic vertebrate was supported by our data.     

Rate of occurrence of transient magnetic field events in U.S. residences

Recent interest in the transient magnetic field events produced by electrical switching events in residential and occupational environments has been kindled by the possibility that these fields may explain observed associations between childhood cancer and wire codes. This paper reports the results of a study in which the rate of occurrence of magnetic field events with 2-200 kHz frequency content were measured over 24 h or longer periods in 156 U.S. residences. A dual-channel meter was developed for the study that, during 20 s contiguous intervals of time, counted the number of events with peak 2-200 kHz magnetic fields exceeding thresholds of 3. 3 nT and 33 nT. Transient activity exhibited a distinct diurnal rhythm similar to that followed by power frequency magnetic fields in residences. Homes that were electrically grounded to a conductive water system that extended into the street and beyond, had higher levels of 33 nT channel transient activity. Homes located in rural surroundings had less 33 nT transient activity than homes in suburban/urban areas. Finally, while transient activity was perhaps somewhat elevated in homes with OLCC, OHCC, and VHCC wire codes relative to homes with underground (UG) and VLCC codes, the elevation was the smallest in VHCC and the largest in OLCC homes. This result does not provide much support for the hypothesis that transient magnetic fields are the underlying exposure that explains the associations, observed in several epidemiologic studies, between childhood cancer and residence in homes with VHCC, but not OLCC and OHCC, wire codes.     

Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility.

A new method for including local conformational flexibility in calculations of the hydrogen ion titration of proteins using macroscopic electrostatic models is presented. Intrinsic pKa values and electrostatic interactions between titrating sites are calculated from an ensemble of conformers in which the positions of titrating side chains are systematically varied. The method is applied to the Asp, Glu, and Tyr residues of hen lysozyme. The effects of different minimization and/or sampling protocols for both single-conformer and multi-conformer calculations are studied. For single-conformer calculations it is found that the results are sensitive to the choice of all-hydrogen versus polar-hydrogen-only atomic models and to the minimization protocol chosen. The best overall agreement of single-conformer calculations with experiment is obtained with an all-hydrogen model and either a two-step minimization process or minimization using a high dielectric constant. Multi-conformational calculations give significantly improved agreement with experiment, slightly smaller shifts between model compound pKa values and calculated intrinsic pKa values, and reduced sensitivity of the intrinsic pKa calculations to the initial details of the structure compared to single-conformer calculations. The extent of these improvements depends on the type of minimization used during the generation of conformers, with more extensive minimization giving greater improvements. The ordering of the titrations of the active-site residues, Glu-35 and Asp-52, is particularly sensitive to the minimization and sampling protocols used. The balance of strong site-site interactions in the active site suggests a need for including site-site conformational correlations.     

Molecular modeling of proteins: a strategy for energy minimization by molecular mechanics in the AMBER force field.

Energy minimization is an important step in molecular modeling of proteins. In this study, we sought to develop a minimization strategy which would give the best final structures with the shortest computer time in the AMBER force field. In the all-atom model, we performed energy minimization of the melittin (mostly alpha-helical) and cardiotoxin (mostly beta-sheet and beta-turns) crystal structures by both constrained and unconstrained pathways. In the constrained path, which has been recommended in the energy minimization of proteins, hydrogens were relaxed first, followed by the side chains of amino acid residues, and finally the whole molecule. Despite the logic of this approach, however, the structures minimized by the unconstrained path fit the experimental structures better than those minimized by constrained paths. Moreover, the unconstrained path saved considerable computer time. We also compared the effects of the steepest descents and conjugate gradients algorithms in energy minimization. Previously, steepest descents has been used in the initial stages of minimization and conjugate gradients in the final stages of minimization. We therefore studied the effect on the final structure of performing an initial minimization by steepest descents. The structures minimized by conjugate gradients alone resembled the structures minimized initially by the steepest descents and subsequently by the conjugate gradients algorithms. Thus an initial minimization using steepest descents is wasteful and unnecessary, especially when starting from the crystal structure. Based on these results, we propose the use of an unconstrained path and conjugate gradients for energy minimization of proteins. This procedure results in low energy structures closer to the experimental structures, and saves about 70-80% of computer time. This procedure was applied in building models of lysozyme mutants. The crystal structure of native T4 lysozyme was mutated to three different mutants and the structures were minimized. The minimized structures closely fit the crystal structures of the respective mutants (less than 0.3 A root-mean-square, RMS, deviation in the position of all heavy atoms). These results confirm the efficiency of the proposed minimization strategy in modeling closely related homologs. To determine the reliability of the united atom approximation, we also performed all of the above minimizations with united atom models. This approximation gave structures with similar but slightly higher RMS deviations than the all-atom model, but gave further savings of 60-70% in computer time. However, we feel further investigation is essential to determine the reliability of this approximation.(ABSTRACT TRUNCATED AT 400 WORDS)