ABR frequency tuning curves in dolphins

Tone-tone masking was used to determine auditory brain-stem response tuning curves in dolphins (Tursiops truncatus) in a simultaneous-masking paradigm. The Q ₁₀ of the curves was as large as 16–19 in the frequency range 64–128 kHz. In the range 45–16 kHz, Q ₁₀ decreased proportionally to the frequency with the bandwidth of the curves being constant, about 3.5–4 kHz at the 10-dB level. Tuning curves below 45 kHz are supposed to reflect broad spectral bandwidth of the probe's effective part which is no longer than 0.5 ms, irrespective of actual probe duration. Tuning curves above 64 kHz are supposed to reflect the real frequency tuning of the dolphin's auditory system.Abbreviations ABR auditory brain stem response - AP action potential     

Analysis of non-linearities in mutation frequency curves

Mutation frequency curves for ultraviolet light and other mutagens often exhibit non-linear, as well as linear components. A common pattern observed for UV-induced reversion of auxotrophy in yeast is a biphasic, linear-quadratic (or higher order) response. The non-linear component in such a biphasic frequency curve can arise in two distinct, but non-mutually exclusive, ways: (i) as a result of the existence of two-hit processes in the molecular mechanism(s) of mutagenesis; and (ii) as a result of the possible stochastic dependence of mutation and killing, such that the probability of clone formation by the mutant cells differs from that of the non-mutant cells in the population. We describe here a simple mathematical method for distinguishing between these two sources of non-linearity. It is based on the calculation of a quantity that we call ‘apparent survival’. This is given, for any mutagen dose x, by the ratio of the mutant yield to the corresponding linear component of mutation frequency. If the apparent survival rises to values greater than unity before declining at high doses, then there must exist positive two-hit (or higher order) components in the mutational mechanism. If the final slope of the apparent survival curve differs from that of the measured survival curve, then there also exists some degree of stochastic dependence between mutation and killing.     

Force production by depolymerizing microtubules: load-velocity curves and run-pause statistics.

Experiments indicate that depolymerization of microtubules generates sufficient force to produce the minus-end-directed transport of chromosomes during mitosis (Koshland et al., 1988). In vitro, analogous transport of kinesin-coated microspheres exhibits a paradoxical effect. Minus-end-directed transport of the microspheres driven by depolymerization is enhanced by the presence of ATP, which fuels the motor action of kinesin driving the microspheres in the opposite direction, toward the plus end of the microtubule. Here we present a mathematical model to explain this behavior. We postulate that a microsphere at the plus end of the microtubule facilitates depolymerization and hence enhances minus-end-directed transport. The force-velocity curve of the model is derived; it has the peculiar feature that velocity is maximal at some positive load (opposing the motion) rather than at zero load. The model is used to simulate the stochastic process of microsphere-facilitated depolymerization-driven transport. Simulated trajectories at low load show distinctive runs and pauses, the statistics of which are calculated from the model. The statistics of the process provide sufficient information to determine all of the model's parameters.     

Analysis of mutant frequency curves and survival curves applied to the AL hybrid cell system

A model is presented for the statistical analysis of survival curves and mutant frequency curves for a hybrid cell system. The derivation of the model is given in the Appendix, and depends on simple assumptions about the distribution of insults, their repair, and the loss of a marker that is not rescued. A single formula (5) is found which relates a survival curve to the mutant frequency curve, i. e., the response curve for production of mutants per 10(5) survivors induced by a mutagen. The analysis is applied to loss of the a1 gene in AL-J1 hybrid cells submitted to Cesium gamma-rays. Previous experimental data using X-rays was reported by Waldren et al. (1986: Proc. Natl. Acad. Sci, USA 83, 4839.) Also, a derived formula (10), which predicts the probability that in a surviving cell a marker is lost and not rescued, will form the basis for testing the validity of the model in the future using new experimental data.     

Assessing mortality changes from size‐frequency curves

The relationship between the instantaneous mortality rate ( Z ) and the instantaneous change in length‐frequency distribution of organisms per unit of animal size (μ _L ) takes the following form: Z  = μ _L k ( L _∞ −  L ) +  k , where k and L _∞ are coefficients of the von Bertalanffy equation, and L is organism size (length). Z and μ_L change coherently when they are measured for a specific size or age class. Therefore, observations of μ _L can provide information on the relative changes in mortality. This is useful when no precise information about animal growth is available and growth curve is assumed to be invariable. This method was tested on a heavily exploited population of St Peter's fish (mango tilapia) Sarotherodon galilaeus in Lake Kinneret, Israel, where large fluctuations in the size structure of the catch have occurred over the past few years. Analysis of the changes in the length‐frequency distributions showed that the changes in μ _L over multiple years estimated for fully exploited fish reflected the respective changes in Z .     

Review: SMCs in the world of chromosome biology- from prokaryotes to higher eukaryotes

The study of higher order chromosome structure and how it is modified through the course of the cell cycle has fascinated geneticists, biochemists, and cell biologists for decades. The results from many diverse technical avenues have converged in the discovery of a large superfamily of chromosome-associated proteins known as SMCs, for structural maintenance of chromosomes, which are predicted to have ATPase activity. Now found in all eukaryotes examined, and numerous prokaryotes as well, SMCs play crucial roles in chromatid cohesion, chromosome condensation, sex chromosome dosage compensation, and DNA recombination repair. In eukaryotes, SMCs exist in five subfamilies, which appear to associate with one another in particular pairs to perform their specific functions. In this review, we summarize current progress examining the roles these proteins, and the complexes they form, play in chromosome metabolism. We also present a twist in the SMC story, with the possibility of one SMC moonlighting in an unpredicted location.     

Words in DNA sequences: some case studies based on their frequency statistics

 One of the critical requirements of data analysis involving large DNA sequences is an effective statistical summarization of those sequences. In this article DNA sequences have been analyzed based on word frequencies. Our analysis focuses on the detection of structural signature of a genome reflected in word frequencies and identification of phylogenetic relationships among different species reflected in the variation of word distributions in their DNA sequences. We have carried out a statistical study of the complete genome of baker's yeast, of various ribosomal RNA sequences from different prokaryotic and eukaryotic organisms and of the full genomes of some bacteriophages. Our exploratory analysis amply demonstrates the usefulness of DNA word frequencies in reducing the dimensionality of large sequences while retaining some of the structural information there that can have biological significance. Some conceptual issues that arise in course of our investigation have been addressed. A few interesting problems related to the statistics of DNA words have been pointed out with some indication of their possible solutions. The work has been partially motivated by the fact that sequence alignment and homology techniques that are quite popular for comparing and analyzing relatively smaller DNA sequences of nearly equal sizes are not applicable to data consisting of large sequences with widely varying sizes, which may contain segments with unknown or no biological functions, and consequently their comparison through functional homology is either impossible or extremely difficult. Received: 15 October 2000 / Revised version: 8 October 2002 Published online: 28 February 2003 Current address: CF186, Salt lake, Calcutta 700064, India Research presented here was supported in part by a grant from Indian Statistical Institute. Key words or phrases: Average linkage clustering – Chernoff's faces – Dendrograms – DNA words – F-ranks of words – F-ratios of words – l ₁-distance – Phylogenetic relationships – Rank correlation – Single linkage clustering     

A new interpretation of the frequency curves associated with ant polymorphism

Summary The frequency curves characterizing all stages in the phylogenetic development of ant polymorphism can be interpreted most simply on the basis of divergence of two size groups of larvae beyond a critical point in larval development. The degree of divergence, and with it the decrease of the medias, depends on the amount of development, or the rate of divergence, following the critical point. The frequency curves characterizing the more elementary stages of polymorphism can be explained on the basis of simple competition among larvae, providing that a fair degree of ovipository periodicity obtains. This interpretation is at present supported principally by inconclusive circumstantial evidence, and it is admitted that other explanations may be found to hold equally well.     

Minor differences in haplotype frequency estimates can produce very large differences in heterogeneity test statistics

Background

Genome wide association (GWA) studies provide the opportunity to develop new kinds of analysis. Analysing pairs of markers from separate regions might lead to the detection of allelic association which might indicate an interaction between nearby genes.

Methods

396,591 markers typed in 541 subjects were studied. 7.8*10¹⁰ pairs of markers were screened and those showing initial evidence for allelic association were subjected to more thorough investigation along with 10 flanking markers on either side.

Results

No evidence was detected for interaction. However 6 markers appeared to have an incorrect map position according to NCBI Build 35. One of these was corrected in Build 36 and 2 were dropped. The remaining 3 were left with map positions inconsistent with their allelic association relationships.

Discussion

Although no interaction effects were detected the method was successful in identifying markers with probably incorrect map positions.

Conclusion

The study of allelic association can supplement other methods for assigning markers to particular map positions. Analyses of this type may usefully be applied to data from future GWA studies.     

Analysis of non-linearities in frequency curves for UV-induced mitotic recombination in wild-type and excision-repair-deficient strains of yeast

Frequency curves for UV-induced mitotic recombination often are linear at low doses. As dose increases, these curves either increase at higher powers of dose and/or reach a maximum induced frequency and then decline. Similar dose-response patterns have been observed previously for mutation. The non-linearities can arise from higher order effects inherent in the molecular mechanisms of mutagenesis and/or from 'delta-effects' (Eckardt and Haynes, 1977a), i.e., differential probabilities of clone formation for mutant and non-mutant cells. Previously, we have shown that one can distinguish between these two possibilities by plotting the ratio of the induced mutant yield to the linear component of frequency as a function of dose (Haynes et al., 1985). In this study, we have used this ratio, a quantity we call 'apparent survival', to analyse the non-linear regions of the dose-response curves for UV-induced mitotic crossing-over and gene conversion in wild-type (RAD) and excision-repair-deficient (rad3) strains of yeast. Plots of apparent survival versus dose reveal the existence of a positive, non-linear component associated with UV-induced gene conversion in RAD, but not rad3, cells. A high dose decline in frequency, which is observed for UV-induced recombination in both strains, can be attributed to delta-effects.     

Derivation of the frequency distributions of cycle durations from continuous labeling curves

In cell populations that are continuously exposed to radioactive thymidine over a long period, all proliferating cells become labeled as they pass through their DNA-replicating phase. The continuous labeling curve (CLC) shows the percentage of labeled cells versus time. Expected CLCs are calculated for cell populations with arbitrary frequency distributions of cycle durations. By optimizing the parameter values of a general probability function in the formula for CLC, frequency distributions of cycle durations are estimated from experimental CLCs. The analysis of several fetal rat tissues shows that the cycle durations vary over quite a wide range within the same tissue.     

Cell property determination from the acoustic microscope generated voltage versus frequency curves

Among the methods for the determination of mechanical properties of living cells acoustic microscopy provides some extraordinary advantages. It is relatively fast, of excellent spatial resolution and of minimal invasiveness. Sound velocity is a measure of the stiffness or Young's modulus of the cell. Attenuation of cytoplasm is a measure of supramolecular interactions. These parameters are of crucial interest for studies of cell motility, volume regulations and to establish the functional role of the various elements of the cytoskeleton. Using a phase and amplitude sensitive modulation of a scanning acoustic microscope (Hillman et al., 1994, J. Alloys Compounds. 211/212:625-627) longitudinal wave speed, attenuation and thickness profile of a biological cell are obtained from the voltage versus frequency or V(f) curves. A series of pictures, for instance in the frequency range 980-1100 MHz with an increment of 20 MHz, allows the experimental generation of V(f) curves for each pixel while keeping the lens-specimen distance unchanged. Both amplitude and phase values of the V(f) curves are used for obtaining the cell properties and the cell thickness profile. The theoretical analysis shows that the thin liquid layer, between the cell and the substrate, has a strong influence on the reflection coefficient and should not be ignored during the analysis. Cell properties, cell profile and the thickness of the thin liquid layer are obtained from the V(f) curves by the simplex inversion algorithm. The main advantages of this new method are that imaging can be done near the focal plane, therefore an optimal signal to noise ratio is achieved, no interference with Rayleigh waves occurs, and the method requires only an approximate estimate of the material properties of the solid substratum where the cells are growing on.     

Optimal Degree of Skew in Cooperative Societies

An optimization model is employed to determine the outcome ofwithin-group conflict in cooperative societies. The model assumesthat selection acts simultaneously on the stronger, dominantmembers of the group to secure more benefits for themselvesat the expense of subordinates, and on subordinates to leavethe group in response to this usurpation if they can do betterelsewhere. When it is in the interest of the dominant to maintainthe group, the dominant will be limited in its opportunity tobias the benefits in its favor by the options available to subordinatesoutside the group. The resulting differences in fitness or netpay-off among group members due to usurpation by dominants definethe degree of skew. Ecological factors affect both the net benefitof grouping and the options for leaving, and thus establishthe limits of skewing. The assumptions and rules governing thisinteraction are first outlined using a game theory approach.A continuous model for predicting the exact degree of skew isthen developed. This analysis shows that the degree of skewincreases when the benefit of group breeding relative to solitarybreeding increases, and when the degree of relatedness amonggroup members increases. Finally, the trade-offs between breedingwith relatives versus nonrelatives are analyzed from a dominantrelative's point of view. The results of two empirical studieson a social bird and a social wasp are compared to the predictionsof these models. The exceptionally good fit to the models isinterpreted as evidence in favor of the "social manipulation"approach to "helping" and "altruism" in cooperatively breedingspecies.