Some comments on coordinate-free and scale-invariant methods in morphometrics

The unusual strategy for comparing biological shapes is to use some kind of superimposition of the two forms under study and then look at the "residuals" as the shape change. In this paper, I take a careful look at this general strategy and point out some subtle but inherent and important pitfalls. Additionally an alternative approach based on Euclidean Distance Matrix representation is presented. It is applicable to two- as well as three-dimensional objects.     

Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme

A method is presented to describe the internal motions of proteins obtained from molecular dynamics or Monte Carlo simulations as motions of normal mode variables. This method calculates normal mode variables by projecting trajectories of these simulations onto the axes of normal modes and expresses the trajectories as a linear combination of normal mode variables. This method is applied to the result of the molecular dynamics and the Monte Carlo simulations of human lysozyme. The motion of the lowest frequency mode extracted from the simulations represents the hinge bending motion very faithfully. Analysis of the obtained motions of the normal mode variables provides an explanation of the anharmonic aspects of protein dynamics as due first to the anharmonicity of the actual potential energy surface near a minimum and second to trans-minimum conformational changes.     

Microsite differentiation in a Mediterranean oak savanna

Abstract. Microscale variation of vegetation was studied in a Mediterranean oak savanna dominated by annual plants at Neve Ya'ar Experimental Station, in the lower Galilee of Israel. Species presence/absence data were recorded in 20 cm x 20 cm quadrats on a 500-quadrat transect. These data were ordinated with Detrended Correspondence Analysis. Soil nitrate, phosphorous, potassium, pH, soil moisture and salinity were determined at 2-m intervals on the 100-m transect, at monthly intervals from November 1981 to April 1982. Litter cover and canopy shade were surveyed in October 1981 and April 1982. A sharp rise in available nitrate occurred in November, following the first winter rains. Patterns in herbaceous vegetation, as expressed by sample ordination scores, correlated best with litter cover in October. This suggested that vegetation pattern in this community may be strongly influenced by environmental conditions at the time of seedling germination and establishment.     

Computer-assisted image analysis of the distributions of peptidergic terminals in the central nucleus of the amygdala: A preliminary study

When viewed under dark-field illumination, peptidergic terminals in sections stained by the Sternberger PAP immunocytochemical method are seen as individual points of light. Under high magnification, the degree of brightness of various areas of immunoreactive terminals is seen to be a function of the density of terminals in these areas. By analyzying the relative brightness of the immunostained central nucleus of the amygdala (CNA) with an EyeCom II PDP-$\text{11}\text{34}$ image analysis system, we have obtained a relative evaluation of the density distribution of neurotensin (NT)-, substance P (SP), VIP-, angiotensin II (AII), m-enkephalin (m-ENK) and somatostatin (SS)-immunoreactive terminals in terms of normal morphology and following a brain lesion. The EyeCom II system divides the presented image into 307200 picture elements (pixels) and assigns one of 256 grey values to the average brightness with each pixel. We have aggregated the grey level frequencies into 5 levels where level 1 corresponds to the highest terminal density and level 5 to the lowest density. At level 1, only NT- and VIP-immunoreactive terminals occupy a significant percentage of the cross-sectional area of the CNA (20%). About 15% of the area of the CNA has VIP terminals with level 5 density. The distributions of the top 20% of the terminal density range of NT, SP, AII and VIP support a classical medial/lateral division of the nucleus. The distribution of the same range of SS- and ENK terminals suggests a dorsoventral division of the CNA. A preliminary study indicates that comparison of grey level frequency histograms generated by image analysis from homologous lesioned and unlesioned sections of the CNA can yield useful information regarding post-lesion changes in the distribution of immunoreactive terminals.     

Estimation of phenological stages and physiological states of grasslands from remote sensing data

Two radiometers measuring reflectance factors have been used at a height of 1.50 m above some grasslands in C. France. The results show that both spectral data are sensitive to the photosynthetic activity of the grassland. Measurements made in April, May, June and July show that grasslands have quite different spectral behaviour according to soil conditions or to grazing level. Grasslands on dry or wet soils may be separated from those of normal soils for which overgrazing and trampling affecting the growth of species, are shown by the different spectral values. Such on the ground remote sensing measurements may then be proposed for evaluating the range of growth and development of different grasslands.Convention C.N.E.S./I.N.A.P-G. ref.: 80/CNES/24 I thank CNES and IGN for the facilities given to assume this experiment. Many thanks to Lynn Erselius, who revised the text. Mr. Lecordix, a student from the Ecole Nationale des Sciences Géographiques and Mr. Besnard, a student from the Orsay University (Plant Biology) helped in the collection and handling of spectral resp, floristical data.     

The Benzodiazepine/GABA Receptor Complex: Molecular Size in Brain Synaptic Membranes and in Solution

Abstract: The molecular size of the benzodiazepine (BZ) receptor in the synaptic membrane of brain cortex (bovine or rat) was determined by an improved version of the radiation inactivation method to be 220,000. An identical size was found simultaneously for the associated γ-aminobutyric acid (GABA) receptor and for the component binding β-carboline esters. It is proposed that all three activities reside in a single protein or protein complex in the membrane. The size in solution, after extraction into Triton X-100 medium from exhaustively washed membranes, was estimated by sedimentation constant (9.4S) and by gel filtration (∼230,000 apparent MW), again with the BZ and GABA binding activities behaving identically. This size applies to the component that undergoes photoaffinity labelling by [³H]flunitrazepam in the membrane, and contains a 51,000 M_r polypeptide as the BZ-binding subunit. It is concluded that a protein complex or oligomer of 200,000–220,000 MW carries a class of BZ-binding sites and an associated class of GABA_A sites.     

DNA protection with the DNA methylase M . BbvI from Bacillus brevis var. GB against cleavage by the restriction endonucleases PstI and PvuII

BamHI fragments of the Bacillus brevis var. GB plasmid pAD1 have been cloned in Escherichia coli HB101 using pBR322 plasmid as a vector. The analysis of the recombinant plasmids showed that additional PstI sites had appeared in cloned fragments of pAD1. Methylation of the recombinant plasmids in vitro by enzymes from B. brevis GB cells blocks cleavage at these additional PstI sites of cloned pAD1 fragments and at the PstI site of pBR322. Among DNA methylases of B. brevis GB, the cytosine DNA methylase M . BbvI is the most likely agent modifying the recognition sequences of PstI. The methylase can modify cytosine residues in PstI or PvuII sites if these recognition sequences are linked to G at 5'- or to C at 3'-termini. In particular, in vitro methylation of the SV40 DNA by B. brevis GB methylases protects one of the two PstI sites and two of the three PvuII sites. The described effect of the protection of the specific PstI and PvuII sites may be used for physical mapping of genomes and DNA cloning.     

Cytogenetic and electrophoretic evidence for a polyploid origin of the basic chromosome number x = 14 in the genusAsphodelus (Liliaceae)

Cytogenetic and electrophoretic analyses on 2n = 28 strains ofAsphodelus cerasiferus strongly suggest that the basic number x = 14 of the genusAsphodelus is of secondary polyploid origin from x = 7.