Ligand-receptor and junction-mediated cell-cell interactions: comparison of the two principles

Two major forms of cell-cell interaction--namely, ligand-receptor interactions and junction-mediated interactions--have different functional implications and naturally supplement each other in the most important tissue processes. The former type of interaction may be defined as distant and mainly "intertissue"; as a rule it determines temporal coordination of cell functioning. The latter is local and preferentially "intratissue"; it determines spatial coordination of cell activity.     

Fold recognition via a tree.

Recently, we developed a pairwise structural alignment algorithm using realistic structural and environmental information (SAUCE). In this paper, we at first present an automatic fold hierarchical classification based on SAUCE alignments. This classification enables us to build a fold tree containing different levels of multiple structural profiles. Then a tree-based fold search algorithm is described. We applied this method to a group of structures with sequence identity less than 35% and did a series of leave one out tests. These tests are approximately comparable to fold recognition tests on superfamily level. Results show that fold recognition via a fold tree can be faster and better at detecting distant homologues than classic fold recognition methods.     

Ligand-receptor relationships in immune regulation

The relationship between ligand, idiotype-bearing ligand-binding T suppressor cells (Ts), and antiidiotypic Ts is discussed. The suppressor pathway involves the activation by ligand of first-order idiotypic Ts (Ts1) which elaborate idiotype-bearing T suppressor factors (TsF). TsF readily induced second-order antiidiotypic TS2 cells. The genetic restrictions imposed on the immune system once perturbed by antigen are evaluated.     

Homologous chromosome pairing.

Commonly accepted precepts are challenged: (1) that homologous chromosome pairing is normally mediated by nuclear envelope attachment sites; (2) that crossover site establishment awaits synaptic completion; and (3) that it is the function of the synaptonemal complex to hold homologues in register so that equal crossing over can occur, and perhaps to provide machinery for the crossover process. Although these views may eventually be shown to be true, it is felt that currently available evidence does not warrant their full acceptance, and that alternatives should be considered. As examples of alternatives the following ideas, with some supporting evidence, are suggested: (1) homologous chromosome pairing (in non-haplont organisms) may be accomplished by chance meeting of homologue segments (followed by establishment of invisible, elastic connectors) at congression for a mitotic metaphase (in many cases perhaps the premeiotic mitosis); (2) crossover sites may be established before, during, or immediately following initiation of synapsis; and (3) the synaptonemal complex may somehow function in the crossover process at the inception of its formation, but its complete deployment throughout each normal bivalent may serve some other role, such as mediation of the binding of sister chromatids apparently required for chiasma maintenance until anaphase I.     

A pairing process.

A stochastic model for the formation of parasite pairs in the definite host is considered. An explicit expression for the expected number of pairs is derived and compared with alternative models.     

Ligand-receptor interactions: detailed evaluation of occupancy-dependent affinity

The exact nature of the curvilinearity of Scatchard plots derived from hormonal and nonhormonal binding systems has not been definitively resolved. Such plots are compatible with heterogeneous receptors with different but fixed affinities and with negatively interacting binding sites resulting in occupancy-dependent affinity. In the current study we examined in detail the effect of receptor occupancy by the ligand on receptor affinity under a variety of experimental conditions. We chose the human lymphocyte-leukoagglutinin (LPHA) system, which closely mimics the IM9-insulin model. Reliable estimates of total binding capacity (728 ng/10(6) cells) essential to our report were calculated from a wide database by the least-squares model. At occupancies greater than or equal to 0.085, receptors are associated with low and fixed affinity (1.5 X 10(6) M-1), whereas at occupancies less than or equal to 0.085, affinity is high and fixed (1.8 X 10(8) M-1) or high but variable (1 X 10(7) M-1 to 1.5 X 10(6) M-1) depending on whether the binding is assumed to be noncooperative or cooperative, respectively. Calculation of receptor-ligand complex dissociation velocity over a wide range of occupancies (0.01-0.40) suggested that occupancy exerts an inversely proportional effect on affinity that is rapid and sustained. Cell activation (DNA synthesis) is initiated at receptor occupancy of approximately equal to 0.004 and is magnified as ligand binding to high affinity receptors increases up to approximately equal to 0.07 occupancy (functional sites), beyond which point further binding (to low affinity sites) becomes increasingly ineffective and cytotoxic (redundant sites). These findings suggest that occupancy influences affinity as postulated by the hypothesis of negative cooperativity. Through this effect occupancy may play a significant role in regulating ligand-induced cell responses.     

Ligand-receptor interaction rates in the presence of convective mass transport.

The rate of binding of a ligand to receptors on the cell surface can be diffusion limited. We analyze the kinetics of binding, diffusion-limited in a stationary liquid, in the presence of convective mass transport. We derive a formula that expresses the reaction kinetics in terms of the mass transfer coefficient. A moderately transport-limited kinetics is not readily recognizable from the shape of the binding curve and may lead to erroneous estimates of the rate coefficients. We apply our results to practically important cases: a cell suspension in a stirred volume of liquid and a confluent cell colony under a laminar stream. Using typical numbers characterizing the ligand-receptor interactions, we show that stirring and perfusion can be important factors determining the reaction rates. With the confluent colony, the early reaction kinetics requires a different treatment, and we provide it for the case of low receptor occupancy. We show that, even with a fast perfusion, a cell monolayer can transiently generate a zone of depletion of the ligand, and that would affect the early stages of the reaction. Our results are expressed in a simple analytical form and can be used for the design and interpretation of experimental data.     

Evidence for splice site pairing via intron definition in Schizosaccharomyces pombe

Schizosaccharomyces pombe pre-mRNAs are generally multi-intronic and share certain features with pre-mRNAs from Drosophila melanogaster, in which initial splice site pairing can occur via either exon or intron definition. Here, we present three lines of evidence suggesting that, despite these similarities, fission yeast splicing is most likely restricted to intron definition. First, mutating either or both splice sites flanking an internal exon in the S. pombe cdc2 gene produced almost exclusively intron retention, in contrast to the exon skipping observed in vertebrates. Second, we were unable to induce skipping of the internal microexon in fission yeast cgs2, whereas the default splicing pathway excludes extremely small exons in mammals. Because nearly quantitative removal of the downstream intron in cgs2 could be achieved by expanding the microexon, we propose that its retention is due to steric occlusion. Third, several cryptic 5' junctions in the second intron of fission yeast cdc2 are located within the intron, in contrast to their generally exonic locations in metazoa. The effects of expanding and contracting this intron are as predicted by intron definition; in fact, even highly deviant 5' junctions can compete effectively with the standard 5' splice site if they are closer to the 3' splicing signals. Taken together, our data suggest that pairing of splice sites in S. pombe most likely occurs exclusively across introns in a manner that favors excision of the smallest segment possible.     

RadCon: phylogenetic tree comparison and consensus

SUMMARY: RadCon is a Macintosh program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information Content of individual trees, the stability of leaves across a set of bootstrap trees, produce the strict basic Reduced Cladistic Consensus profile of a set of trees and convert a set of trees into its matrix representation for supertree construction. AVAILABILITY: The program is free and available at http://taxonomy.zoology.gla.ac.uk/ approximately jthorley/radcon/radcon.html.     

Rovibrational energy and spectroscopic constant calculations of complexes pairing via dihydrogen bonds

In the present investigation, we performed a thorough study of potential energy curves, rovibrational spectra, and spectroscopic constants for complexes pairing via dihydrogen bonds. In particular, we dealt with LiH???HX (X = F, CN, CCH, CCF, CCCl) complexes by employing accurate electronic energy calculations at the MP2/aug-cc-pVDZ level of theory. Following this, the Numerov method was applied to solve the nuclear Schrödinger equation, thus obtaining spectroscopic constants and rovibrational spectra. Good linear correlation between the magnitudes of the interaction energies for interaction of HX with LiH, and the most positive electrostatic potentials of hydrogen in HX, was established.     

Adenine-guanine base pairing ribosomal RNA.

Analyses of secondary structures proposed for ribosomal RNA's show that, of the different kinds of base pairs directly adjoining the ends of postulated double-helical regions, only A-G with A at the 5' end significantly exceeds the number expected for a random base distribution. An A(syn)-G(trans) hydrogen-bonded basepair is proposed. This could fit at the end of an undistorted double helix, but would prevent further base stacking, thus favoring a break in the double helix to produce a non-linear tertiary structure.     

Ligand-receptor interaction. Klotz-Hunston problem for two classes of binding sites and its solution

The problem of the affinity and quantity determination of two classes of binding sites for ligand-receptor interaction using either Scatchard or Klotz plots was considered. Klotz and Hunston previously solved this problem only for the case of a representation of experimental data using the Scatchard plot. Since their publication, it was the common view that only the use of the Scatchard plot allows solving this problem. However, in some cases, using the Klotz plot is more convenient for a representation of experimental data concerning ligand-receptor interaction, though usually, this plot was used only for the evaluation of receptor affinity with one class of binding sites. In the present paper, it was demonstrated that Klotz plot also could be used for the evaluation affinity and quantity of two classes of binding sites.     

Numerical classification techniques applied to forest tree distribution data. I. A comparison of methods

Distribution data for 111 mainly sclerophyll forest tree species in southern and eastern Australia were analysed to detect possible phytogeographic provinces. The suitability of fourteen methods of numerical classification was assessed. Overall, the Kulczynski (1927) similarity coefficient together with the flexible clustering strategy (β= 0.25) (Lance & Williams 1967) and the asymmetric information statistic (Dale, Lance & Albrecht 1971) were considered to produce the most satisfactory results.     

ISH-facilitated analysis of meiotic bivalent pairing.

Chiasmata constitute one of the cornerstones of sexual reproduction in most eukaryotes. They mediate the reciprocal genetic exchange between homologues and are essential to the proper orientation of the homologous centromeres in meiosis I. As markers of recombination, they offer a cytological means of mapping. Rather than trying to accurately count individual chiasmata, we have examined properties of the mathematical relationship between frequencies of nonadorned disomic configurations in meiosis (ring, rods, and univalents) and the probabilities at which arms of the respective chromosomes are chiasmate (one or more chiasma per arm). Numerical analyses indicated that conventionally analyzed bivalents with nonidentified arms yield statistically biased estimates of chiasma probabilities under a broad range of circumstances. We subsequently analyzed estimators derived from adorned configurations with ISH-marked arms, which were found to be statistically far superior, and with no assumptions concerning interference across the centromere. We applied this methodology in the study of chromosomes 16 and 23 of cotton (Gossypium hirsutum), and estimated their arm lengths in centimorgans. The results for chromosome 23, the only one of the two chromosomes with a documented RFLP map, were consistent with the literature. Similar molecular-meiotic configuration analyses can be used for a wide variety of eukaryotic organisms and purposes: for example, providing far more powerful meiotic comparisons of genomes of chromosomes, and a rapid means of evaluating effects on recombination. Key words : meiotic configurations, chiasma frequencies, in situ hybridization, cotton.     

Centromere pairing precedes meiotic chromosome pairing in plants

Meiosis is a specialized eukaryotic cell division, in which diploid cells undergo a single round of DNA replication and two rounds of nuclear division to produce haploid gametes. In most eukaryotes, the core events of meiotic prophase I are chromosomal pairing,synapsis and recombination. To ensure accurate chromosomal segregation, homologs have to identify and align along each other at the onset of meiosis. Although much progress has been made in elucidating meiotic processes, information on the mechanisms underlying chromosome pairing is limited in contrast to the meiotic recombination and synapsis events. Recent research in many organisms indicated that centromere interactions during early meiotic prophase facilitate homologous chromosome pairing, and functional centromere is a prerequisite for centromere pairing such as in maize. Here, we summarize the recent achievements of chromosome pairing research on plants and other organisms, and outline centromere interactions, nuclear chromosome orientation,and meiotic cohesin, as main determinants of chromosome pairing in early meiotic prophase.     

Role of stimulus-stimulus pairing in matching-to-sample procedure: cross-species comparison of humans and pigeons

The present experiment examined whether, in a matching-to-sample (MTS) procedure, a relation between two stimuli, a sample and a comparison, could be established as a result of just stimulus–stimulus pairing, even if back up reinforcers were never provided for the conditional relation between the sample and comparison stimuli, but rather only for the comparison stimulus. A procedure called “pseudo matching-to-sample” was used in which, when S1 was presented as a sample stimulus, two comparison stimuli (C1 and C2) were presented, and only responses to C1 were reinforced. Conversely, when S2 was presented, only responses to C3 (and not C4) were reinforced. In other words, organisms experiencing this procedure could discriminate C1 from C2, and C3 from C4, by simple discrimination without regard to the conditional sample stimuli. In order to examine cross-species differences, responding by humans in this procedure was compared to that by pigeons. Although the humans developed a discriminative function for the sample stimuli, that is, the humans’ responding was affected by both the sample stimuli and the reinforcers, responding by the pigeons was affected solely by the reinforcers. These data suggest that, in this procedure, humans (but not pigeons) are able to learn relations among stimuli simply as a result of stimulus–stimulus pairing.     

热带森林乔木种群分布格局及其研究方法的比较

应用样地个体数为基础的方差／均值比率、Ｍｏｒｉｓｉｔａ分散指标,以及以个体距离为基础的最近邻体法、复合个体距离分析法对海南岛吊罗山山地雨林８个主要种群分布格局进行了比较研究．结果表明,８个种群为聚集或随机分布,４种测定方法中以复合个体距离分析法较好．     

Real-time Monitoring of Ligand-receptor Interactions with Fluorescence Resonance Energy Transfer

FRET is a process whereby energy is non-radiatively transferred from an excited donor molecule to a ground-state acceptor molecule through long-range dipole-dipole interactions¹. In the present sensing assay, we utilize an interesting property of PDA: blue-shift in the UV-Vis electronic absorption spectrum of PDA (Figure 1) after an analyte interacts with receptors attached to PDA^2,3,4,7. This shift in the PDA absorption spectrum provides changes in the spectral overlap (J) between PDA (acceptor) and rhodamine (donor) that leads to changes in the FRET efficiency. Thus, the interactions between analyte (ligand) and receptors are detected through FRET between donor fluorophores and PDA. In particular, we show the sensing of a model protein molecule streptavidin. We also demonstrate the covalent-binding of bovine serum albumin (BSA) to the liposome surface with FRET mechanism. These interactions between the bilayer liposomes and protein molecules can be sensed in real-time. The proposed method is a general method for sensing small chemical and large biochemical molecules. Since fluorescence is intrinsically more sensitive than colorimetry, the detection limit of the assay can be in sub-nanomolar range or lower⁸. Further, PDA can act as a universal acceptor in FRET, which means that multiple sensors can be developed with PDA (acceptor) functionalized with donors and different receptors attached on the surface of PDA liposomes.