Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method "Curves," developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels ("dials") for each torsional parameter and "windows" on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2 degrees structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.     

Breeding Systems in American and Asian Trillium Species by Means of Chromosome Analyses

Abstract Species of Trillium have a disjunct distribution occurring in both North America and eastern Asia. In North America all 36 species are diploid. The 11 species of eastern Asia, however, include only a single diploid with all the other species being polyploids. Why do different patterns of speciation develop in North America and in eastern Asia? The breeding systems of populations in the North American T. erectum, T. grandiflorum and T. ovatum , and in Asian T. kamtschaticum were investigated by estimating the inbreeding coefficient from cold-induced banding patterns which reveal homozygotes and heterozygotes. From the analyses of the inbreeding coefficients, T. erectum, T. grandiflorum and the Pacific coastal species, T. ovatum are predominantly inbreeding species. T. ovatum populations from the Rocky Mountain region are outbreeders. However the Japanese species, T. kamtschaticum has a mixture of outbreeding and inbreeding among populations. The development of polyploid systems in Asia is possibly the result of the diversity of the breeding systems among the populations. The shift from outbreeding to inbreeding appears to be an important key step in the occurrence of poliploids by hybridization between the different species.     

Occurrence of rye (Secale cereale) 350-family DNA sequences inAgropyron and otherTriticeae

Evidence is presented that in the R and P genomes (Secale cereale andAgropyron cristatum, respectively) of theTriticeae there exist closely related 350-family DNA sequences in the terminal heterochromatin. This observation is compared to the relationships between these two genomes derived from a comparison of theNor and5 S DNA loci as well as the available data on morphological characters, chromosome pairing, and isozyme studies. It is concluded that the R and P genomes are not closely related and that the common presence of very similar 350-family DNA sequences reflects the parallel amplification of this family of DNA sequences.     

The cytogeographical distribution pattern ofAllium (Alliaceae) in the Greek Peninsula and Islands

Greece is considered as a secondary centre of evolution for the genusAllium since it possesses about 50% of the species known from the whole Flora Europaea area. In the present investigation 44 GreekAllium spp. have been studied and new chromosome counts are reported from 40 populations and 17 species. The distribution of the different cytotypes (x = 7, x = 8, x = 11 and 2n = 2x, 3x, 4x, 5x, 6x, 7x) in Greece is discussed. From the four phytogeographical subdivisions recognized, South continental Greece shows the greatest species and karyotype diversity. This phenomenon is probably due to the geographical position and to the geological history of this area which has received species and populations from different directions. Subsequently, hybridization apparently has been of evolutionary importance.The genusAllium in Greece I.     

Decreased fertility in related females heterozygous for the 1/29 chromosome translocation

Eighteen heifers and 120 cows which were descendants of a presumed 1/29 carrier Simmental bull were karotyped. Nine heifers (50%) and 48 cows (40%) were found to be heterozygous for the 1/29 translocation (59, XX, t(1q;29q)). The other animals were chromosomally normal (i.e., 60, XX) or not karotyped. The 48 1/29 cows were compared with 72 chromosomally normal cows with regards to days to first conception, calving interval, percentage of calves conceived, percentage of calves weaned and production efficiency (% calved conceived × % calved weaned). Nine carrier heifers were compared to the nine noncarrier heifers as to pregnancy status. Carrier, noncarrier and nonkarotyped relatives were compared to each other and to contemporary females with regard to pregnancy status at their initial exposure to males. The percentage of calves conceived (calving efficiency) in the 72 noncarrier and the 48 females heterozygous for the 1/29 translocation were 81.5 and 74.8%, respectively (P<0.07). Although days to first conception was longer and percentage of calves weaned and production efficiency were lower in the female heterozygous for the 1/29 translocation, the differences were not statistically different (P>0.10) from the noncarriers. Pregnancy rate was 44.4 and 66.7% (P>0.10) for nine carrier and nine noncarrier heifers, respectively. The pregnancy rate of carrier (65.4%), noncarrier (73.2%) and nonkarotyped (77.8%) relatives of this sire at their mating as yearlings, did not differ (P>0.10). The pregnancy rate as yearlings of carrier females (65.4%) and contemporary heifers (79.8%) did differ (P<0.05). Comparing the pregnancy rate as yearlings of all descendants (72.0%) of the Simmental sire to contemporary heifers (79.8%), a significant decrease (P<0.05) was found indicating that fertility of this sire may have been lower than other sires or that other factors beside the translocation affected fertility.     

The convergent trajectories of bird communities along ecological successions in european forests

Summary There is much more variation in the composition of bird communities in the earlier open and semi-open seral stages of ecological successions in forested landscapes of Europe than later on in preforested and forested climactic stages. The demonstration of this trend is achieved from the study of four habitat gradients, two in the mediterranean region (Provence and Corsica) and two in central Europe (Burgundy, France and Poland). A multivariate analysis has been used to illustrate the dynamics of communities along these succession. Displays of the results in bivariate space as well as an illustration of the distributional profiles of some of the most characteristic species show that: i) there is a discrimination between the two mediterranean gradients and the two medioeuropean ones and ii) each succession starts with a very distinct set of species and then the four gradients regularly converge in the last climactic stage where there is almost no discrimination between communities. These results are discussed in the light of the history of European biotas during the Pleistocene. The reason why there is more variation in species composition in the earlier seral stages than in the later forested stages are discussed according to current theories on the role of habitat selection on speciation processes.     

五种恙螨染色体核型的研究

恙螨染色体的研究迄今仅Shirai等(1984)简要地报道了三种纤恙螨的染色体核型。本实验采用压片法和改良空气干燥法,研究观察五种恙螨有丝分裂染色体核型。初静止化蛹1—3天的成蛹阶段是制作恙螨有丝分裂染色体标本的最佳虫期。微红纤恙螨,地里纤恙螨和巨螫齿恙螨染色体数目为2n=14;苍白纤恙螨和小板纤恙螨为2n=16。染色体呈大小不等的小棒状,单着丝粒,但多不清晰,仅可见着丝点区浅染。部分核型出现染色体异型现象。核型性别未明,性别决定机制不清。     

The cytogenetic and hepatotoxic effects of dioxin on mouse liver cells

The cytogenetic and hepatotoxic effects of 2,3,7,8-tetrachlorodibenzo p-dioxin (TCDD) on mouse liver cells were investigated. Male C57BL/6J strain mice, which have TCDD receptors, were given single intraperitoneal injections of 25, 37.5, 75 and 150 g of TCDD/kg body weight or corn oil carrier alone. Two-thirds hepatectomies were carried out at 1 or 7 days after injection and chromosomal aberrations and mitotic indexes of the regenerating hepatocytes were scored 54 hr after hepatectomy. Liver sections from additional intact mice were studied for TCDD-hepatotoxicity at 1, 7 and 30 days after injection. The three high doses of TCDD caused hepatotoxicity with necrosis of liver cells and focal architectural collapse by 30 days after injection. No evidence was obtained of an increase in the frequency of chromosomal structural aberrations at doses that allowed sufficient mitotic activity for cytogenetic evaluation. We conclude that TCDD is not a clastogen for mouse hepatocytes, although high doses cause marked hepatocellular necrosis.Abbreviations CSD chromosome deletion - META metacentric chromosome - TCDD 2,3,7,8-tetrachlorobenzo-p-dioxin     

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.     

A function describing all-sized trunk diameter distribution in warm-temperate rain forests

A simple relation (v-lnB) (u-lnx)=c was recognized betweenx as dbh (or individual basal area) andB as the cumulative basal area abovex, for various stands of warm-temperate rain forests of Yakushima Island, southern Japan (v, u andc, parameters). The model parameters explained a difference in the pattern of stand development between secondary succession after clear-felling and gap regeneration within primary forests.