Algorithms for identifying local molecular sequence features

Efficient algorithms are described for identifying local molecularsequence features including repeats, dyad symmetry pairingsand aligned matches between sequences, while allowing for errors.Specific applications are given to the genomic sequences ofthe Epstein-Barr virus, Varicella-Zoster virus and the bacteriophages and T7. Received on October 6, 1987; accepted on December 13, 1987     

FastMG: a simple,fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

Background

Amino acid replacement rate matrices are a crucial component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Ideally, the rate matrix reflects the mutational behavior of the actual data under study; however, estimating amino acid replacement rate matrices requires large protein alignments and is computationally expensive and complex. As a compromise, sub-optimal pre-calculated generic matrices are typically used for protein-based phylogeny. Sequence availability has now grown to a point where problem-specific rate matrices can often be calculated if the computational cost can be controlled.

Results

The most time consuming step in estimating rate matrices by maximum likelihood is building maximum likelihood phylogenetic trees from protein alignments. We propose a new procedure, called FastMG, to overcome this obstacle. The key innovation is the alignment-splitting algorithm that splits alignments with many sequences into non-overlapping sub-alignments prior to estimating amino acid replacement rates. Experiments with different large data sets showed that the FastMG procedure was an order of magnitude faster than without splitting. Importantly, there was no apparent loss in matrix quality if an appropriate splitting procedure is used.

Conclusions

FastMG is a simple, fast and accurate procedure to estimate amino acid replacement rate matrices from large data sets. It enables researchers to study the evolutionary relationships for specific groups of proteins or taxa with optimized, data-specific amino acid replacement rate matrices. The programs, data sets, and the new mammalian mitochondrial protein rate matrix are available at http://fastmg.codeplex.com.     

The control of multi-muscle systems: human jaw and hyoid movements

A model is presented of sagittal plane jaw and hyoid motion based on the model of motor control. The model, which is implemented as a computer simulation, includes central neural control signals, position- and velocity-dependent reflexes, reflex delays, and muscle properties such as the dependence of force on muscle length and velocity. The model has seven muscles (or muscle groups) attached to the jaw and hyoid as well as separate jaw and hyoid bone dynamics. According to the model, movements result from changes in neurophysiological control variables which shift the equilibrium state of the motor system. One such control variable is an independent change in the membrane potential of -motoneurons (MNs); this variable establishes a threshold muscle length () at which MN recruitment begins. Motor functions may be specified by various combinations of s. One combination of s is associated with the level of coactivation of muscles. Others are associated with motions in specific degrees of freedom. Using the model, we study the mapping between control variables specified at the level of degrees of freedom and control variables corresponding to individual muscles. We demonstrate that commands can be defined involving linear combinations of change which produce essentially independent movements in each of the four kinematic degrees of freedom represented in the model (jaw orientation, jaw position, vertical and horizontal hyoid position). These linear combinations are represented by vectors in space which may be scaled in magnitude. The vector directions are constant over the jaw/hyoid workspace and result in essentially the same motion from any workspace position. The demonstration that it is not necessary to adjust control signals to produce the same movements in different parts of the workspace supports the idea that the nervous system need not take explicit account of musculo-skeletal geometry in planning movements.This article was processed by the author using the LAT_EX style file pljour2 from Springer-Verlag.     

Different binding of RNA polymerase to individual promoters

Summary The amount of E. coli RNA polymerase which can be bound to individual promoters on pgal and dgal phage DNA in a stable heparin-resistant form was measured by assessing its capacity to transcribe, upon addition of the nucleoside triphosphates, the RNA sequences starting at these promoters. These RNA species were analysed by competition hybridization to separated single strands of , pgal and dgal phage DNA.Individual promoters bind, at saturation, different numbers of polymerase molecules. From the amount of polymerase necessary to saturate all promoters (Fig. 3), from the proportions of RNA synthesized at the individual promoters (Table 1) and from the amounts of -³²P-ATP or-GTP label incorporated into the different RNA species (Tables 2 and 3) we calculate polymerase storage capacities for the promoters as follows: gal: 6 molecules; l-strand specific: 3–5 molecules starting with ATP and 1 molecule starting with GTP; r-strand specific: 3–5 molecules starting with ATP (and perhaps one molecule starting with GTP); these estimates are lower limits and may be too small by a factor of up to three.The heparin resistant binding of six polymerase molecules to the gal promoter is dependent on CGA protein and cAMP, but ATP and GTP can allow one polymerase to bind to the same site or to a very close one.Several parameters of polymerase binding are different with the individual promoters tested.     

Construction in vitro of "phage-plasmid" chimerae: a new tool to analyse the mechanism of plasmid maintenance.

Summary In this paper, we report the construction in vitro of chimerae between lambdoid replacement vectors (Murray et al., 1977) and the miniF Ap^r plasmid: pSC138 (Timmis et al., 1975). F recombinants were shown to be chimerae between the and the F replicons. By genetical tests, we have demonstrated that both and F replication mechanisms are functional: the F recombinant behaves as a non defective plaque forming phage on sensitive bacteria and establishes itself as a stable plasmid on recA F^- homoimmune bacteria. In the extra-chromosomal state, the F recombinant apparently retains the controlled autonomous replication and the FI incompatibility characteristics of the F plasmid. The potential experimental uses of these phages are discussed.     

Integrated likelihood functions for non-Bayesian inference

Consider a model with parameter = (, ), where is the parameterof interest, and let L(, ) denote the likelihood function. Oneapproach to likelihood inference for is to use an integratedlikelihood function, in which is eliminated from L(, ) by integratingwith respect to a density function (|). The goal of this paperis to consider the problem of selecting (|) so that the resultingintegrated likelihood function is useful for non-Bayesian likelihoodinference. The desirable properties of an integrated likelihoodfunction are analyzed and these suggest that (|) should be chosenby finding a nuisance parameter that is unrelated to and thentaking the prior density for to be independent of . Such anunrelated parameter is constructed and the resulting integratedlikelihood is shown to be closely related to the modified profilelikelihood.     

Evolutionary change of restriction sites under unequal rates of nucleotide substitution among the three positions of codons

Summary Under the assumption of unequal rates of nucleotide substitution among the three positions of codons, mathematical formulas are derived for the probability that a restriction site observed at time 0 in a DNA sequence will be present at time t, the probability that a new restriction site will emerge at a particular place in two descendant sequences, and the proportion of identical restriction sites between two such sequences. All three quantitites are shown to be larger for the case of unequal rates than for the case of equal rates. As a consequence, estimates of nucleotide divergence (2t) between two sequences based on restriction-site data tend to be lower than the actual values of the assumption of equal rates is made but actually does not hold. However, the degree of underestimation is slight if 2t is 0.10 or smaller. The underestimation can be serious when 2t becomes 0.20 or larger, particularly if the substitution rates at the three codon positions are very different or if transitional substitution occurs more frequently than transversional substitution. The underestimation is more serious for four-base enzymes than for sixbase enzymes.     

A temperature sensitive Reca protein of Escherichia coli

Summary The temperature sensitive allele recA200 has been cloned into the multiple copy number plasmid pBR322 and the gene product isolated. The purified RecA200 protein is temperature sensitive in ability to cleave the phage and LexA repressors in vitro and also in ability to promote a successful search for homology between single stranded DNA and a homologous duplex leading to D-loop formation. However, at the non-permissive temperature the RecA200 protein has approximately wild type single stranded DNA dependent ATPase activity and ability to promote pairing between homologous single DNA strands. The demonstration that the temperature sensitivity in vivo can be correlated with the temperature sensitive cleavage of the and LexA repressors in vitro and also with D-loop formation shows that these in vitro reactions, which require large amounts of RecA protein, are not carried out by trace amounts of contaminating proteins.     

Projecting population-level responses of mysids exposed to an endocrine disrupting chemical

To fully understand the implications of a chemical's effecton the conservation of a species, effects observed at the physiologicalor individual level must be expressed in terms of the population.Since long-term field experiments are typically not feasible,vital rates such as survival and reproduction of individualorganisms are measured in life table response experiments (LTRE)and employed to extrapolate the effects of a pollutant on thepopulation. The population-level response of the mysid, Americamysisbahia, to varying concentrations of methoprene (0, 4, 8, 16,31, 62 µg/L) was determined using age-structured populationmodels. Models were parameterized from the results of an LTREconducted throughout the entire mysid life cycle. A density-independentmatrix model with time invariant demographic parameters wasdeveloped to measure the change in population growth rate, ,with change in methoprene concentration. The values of weregreater than one for all methoprene concentrations, indicatingthat populations exposed to the concentrations reported herewould not become extinct. However, a general decrease in occurredwith increasing methoprene concentration and would result inreduced population sizes. Sensitivity and decomposition analyseswere conducted to determined the relative roles of the vitalrates on altered population growth rates and determined thatimpaired reproduction was the primary influence on the observeddecrease in . The model constructed was a useful tool for linkingthe individual-level effects to the population-level consequencesof methoprene exposure on mysids, as well as defining the mechanism(reduced reproduction) responsible for the observed effectson population.     

Isolation and characterization of lambda b221poriCasnA, a plaque-forming specialized transducing phage carrying the origin of replication of the Escherichia coli chromosome

Summary A specialized transducing phage, b221poriCasnA has been isolated carrying oriC the origin of chromosomal replication of Escherichia coli. All phage genes required for lytic growth are retained, thus the phage is capable of lytic growth. The presence of the oriC locus confers upon infecting phage DNA the ability to replicate as a plasmid using only host DNA replication functions. The presence of both oriC and asnA markers has allowed the development of a plaque assay for origin function which can be used to identify mutants at these loci. Comparison of restriction endonuclease cleavage sites present on b221poriCasnA DNA to those on tis parent, b221 rex::Tn10 suggests the steps involved in the formation of the transducing phage.     

Normal expression of the viral gene N interferes with growth of bacteriophage lambda in Escherichia coli 15T-.

Summary Growth of and of some lambdoid phages is considerably inhibited on strain 3057 derived from E. coli 15T^-. Mutants of which overcome this inhibition map in gene N. Some of these hty mutants are temperature sensitive for growth on E. coli K12. Thus plating of on strain 3057 allows one to isolate temperature sensitive N mutants. The hty mutants produce less than normal N activity as judged by their low efficiency of plating on a nus ^- host and by the extended latent period of some of them on normal hosts. The inability of strain 3057 to propagate can be at least partially reversed by addition of thymidine to the medium and the growth difference between hty and in 3057 increases with decreasing thymidine concentration. The amount of DNA produced by in 3057 at low thymidine concentration is lower than that produced by hty under the same conditions. Only a small percentage of the DNA produced by in 3057 is packaged into viable phage particles. This suggests that not only produces less DNA in 3057 than hty but that an important part of the DNA in 3057 is in a form which can not be packaged or which is noninfective for other reasons. A hypothesis is discussed that hty mutations enable to grow on E. coli 15T^- at low thymidine concentration because they lead to reduction in the number of single strand nicks in the DNA by reducing the intracellular endonuclease activity. Under permissive conditions conditional lethal N mutants are favored for growth on 3057 over N ⁺ which confirms the idea that N activity or the activity of a gene under N control interferes with growth in 3057 at low thymidine concentration.     

PCCA: a program for phylogenetic canonical correlation analysis

Summary: PCCA (phylogenetic canonical correlation analysis)is a new program for canonical correlation analysis of multivariate,continuously valued data from biological species. Canonicalcorrelation analysis is a technique in which derived variablesare obtained from two sets of original variables whereby thecorrelations between corresponding derived variables are maximized.It is a very useful multivariate statistical method for thecalculation and analysis of correlations between character sets.The program controls for species non-independence due to phylogenetichistory and computes canonical coefficients, correlations andscores; and conducts hypothesis tests on the canonical correlations.It can also compute a multivariate version of Pagel's , whichcan then be used in the phylogenetic transformation. Availability: PCCA is distributed as DOS/Windows, Mac OS X andLinux/Unix executables with a detailed program manual and isfreely available on the World Wide Web at: http://anolis.oeb.harvard.edu/~liam/programs/. Contact: lrevell{at}fas.harvard.edu Associate Editor: Keith Crandall     

Evaluation of the lambda model for human postural control during ankle strategy

An accurate modeling of human stance might be helpful in assessing postural deficit. The objective of this article is to validate a mathematical postural control model for quiet standing posture. The postural dynamics is modeled in the sagittal plane as an inverted pendulum with torque applied at the ankle joint. The torque control system is represented by the physiological lambda model. Two neurophysiological command variables of the central nervous system, designated and , establish the dynamic threshold muscle at which motoneuron recruitment begins. Kinematic data and electromyographic signals were collected on four young males in order to measure small voluntary sway and quiet standing posture. Validation of the mathematical model was achieved through comparison of the experimental and simulated results. The mathematical model allows computation of the unmeasurable neurophysiological commands and that control the equilibrium position and stability. Furthermore, with the model it is possible to conclude that low-amplitude body sway during quiet stance is commanded by the central nervous system.     

Mimetization of the elastic properties of cancellous bone via a parameterized cellular material

Bone tissue mechanical properties and trabecular microarchitecture are the main factors that determine the biomechanical properties of cancellous bone. Artificial cancellous microstructures, typically described by a reduced number of geometrical parameters, can be designed to obtain a mechanical behavior mimicking that of natural bone. In this work, we assess the ability of the parameterized microstructure introduced by Kowalczyk (Comput Methods Biomech Biomed Eng 9:135–147, 2006. doi: 10.1080/10255840600751473) to mimic the elastic response of cancellous bone. Artificial microstructures are compared with actual bone samples in terms of elasticity matrices and their symmetry classes. The capability of the parameterized microstructure to combine the dominant isotropic, hexagonal, tetragonal and orthorhombic symmetry classes in the proportions present in the cancellous bone is shown. Based on this finding, two optimization approaches are devised to find the geometrical parameters of the artificial microstructure that better mimics the elastic response of a target natural bone specimen: a Sequential Quadratic Programming algorithm that minimizes the norm of the difference between the elasticity matrices, and a Pattern Search algorithm that minimizes the difference between the symmetry class decompositions. The pattern search approach is found to produce the best results. The performance of the method is demonstrated via analyses for 146 bone samples.     

Lambda phage mutants insensitive to temperature-sensitive repressor

Summary Weak-virulent mutants of temperate coli-phage were isolated which can grow on the CIts lysogen producing a temperature-sensitive repressor but which cannot grow on the wild type lysogen producing a normal repressor.Genetic analysis on the mutants shows that their weak-virulence is attributable to two mutations, one (virL) in the region between sus N₂₁₃ and c ₄₇ and the other (virR) in the region between c ₁ and sus O₈. Both mutations are located within the region of non-homology between and imm ⁴³⁴ phages.True virulent mutants which can grow on the wild type lysogen can be obtained easily from the weak-virulent mutant by an additional mutation, virC in a region very close to virR. The virulent mutants obtained are similar to the classical vir mutant (Jacob and Wollman, 1954). The virL and virR mutations are probably operator mutations which render the genome insensitive to the repressor.This work was reported at the XII th International Congress of Genetics, held in Tokyo, on August 23, 1968.     

Excitation wavelengths for fura 2 provide a linear relationship between [Ca(2+)] and fluorescence ratio

We proposed andtested the use of nontraditional excitation wavelengths(₁ and ₂) and an emission wavelength(_em) to define conditions under which free calciumconcentration and a fluorescence ratio are linearly related.Fluorescence spectra were determined for aqueous solutions thatcontained 25 µM fura 2, 125 mM K⁺, and either 0 mM or 0.1 mM Ca²⁺. Effectively linear relationships between[Ca²⁺] and a fluorescence ratio, i.e., <5% bias when[Ca²⁺]  5 × dissociation constant, were apparentwhen ₁  400 nm, ₂  370 nm, and_em  510 nm. Combinations with longer ₁and _em and/or with shorter ₂ reduced thisbias further. Although the method described does not obviate thecomplications that surround the correction for fluorescence background,choosing a nontraditional combination of excitation and emissionwavelengths offers several practical advantages over more traditionalfura 2 fluorescence methodologies in a variety of experimental settings.

     

Occurrence of mycosporine-like amino acids in the red-tide dinoflagellate Alexandrium excavatum: UV-photoprotective compounds?

Water extracts of the red-tide dinoflagellate Alexandrium excavatumgrown at ‘high’ light intensity (200 µE m^–2s^–1) show a broad absorbance maximum in the UV regionof the spectrum (310–360 nm). Using TLC and reverse-phaseHPLC a series of mycosporine-like amino acids have been characterized:mycosporine-glycine (_max = 310 nm), palythine (_max = 320 nm),asterina-330 (_max = 330 nm), shinorine (_max = 334 nm), porphyra-334(_max= 334 nm), palythenic acid (_max = 337 nm) and the isomericmixture of usujirene and palythene (_max = 359 nm). From theobserved spectral changes during transference from ‘low’(20 µE m^–2 s^–1) to ‘high’ (200µE m^–2 s^–1) light intensities and vice versa,the series of compounds are supposed to be biogenically relatedto one another. The presence of these compounds in A.excavatumis discussed in relation to their possible role in the photoprotectionto deleterious UV radiation.