Reducing ambiguity in describing plant–insect interactions: "preference", "acceptability" and "electivity"

Ecologists and evolutionary biologists have a common interest in plant–insect interactions. Ecologists develop terminology describing patterns of association between plants and insects, while evolutionary biologists use the same words to denote potentially heritable traits of individuals. Use of the same terms to describe both traits of the interaction and traits of the organisms hinders communication. An example is "preference", often used by ecologists to denote properties of the plant–insect interaction and by behavioural or evolutionary biologists to denote insect traits. The existing term "electivity" could be incorporated into the lexicon of plant–insect interactions to supplant the ecological use of "preference". The term "preference" would then denote a behavioural trait of the insect. The mirror-image trait of the plant would be "acceptability". This could be a step towards a common terminology that would be usable by both ecologists and evolutionists.     

"Nonclassic" cytologic signs of cervical condyloma. A case-control study

The association between "nonclassic" cytologic signs of condyloma and human papillomavirus (HPV) infection in women with negative Papanicolaou smears was analyzed via a case-control study. The cytologic signs considered were mild koilocytosis, mild dyskeratosis, binucleation or multinucleation, cleared cytoplasm and nuclear hyperchromatism. The Papanicolaou smears of 166 cases that showed colposcopic and histologic evidence of HPV infection (but whose smears lacked the classic cytologic signs of condyloma) and 166 controls that were negative colposcopically were randomly admixed and blindly reviewed by a panel of cytologists. A significant association to HPV infection was observed for all of the nonclassic signs studied, but multivariate analysis showed a weakly independent association only for mild koilocytosis. The sensitivity (0.46) and the specificity (0.87) of these nonclassic signs were not satisfactory. The utility of selecting women with negative Papanicolaou smears for colposcopy on the basis of these signs is discussed.     

Predicting signatures of "synthetic associations" and "natural associations" from empirical patterns of human genetic variation

Genome-wide association studies (GWAS) have in recent years discovered thousands of associated markers for hundreds of phenotypes. However, associated loci often only explain a relatively small fraction of heritability and the link between association and causality has yet to be uncovered for most loci. Rare causal variants have been suggested as one scenario that may partially explain these shortcomings. Specifically, Dickson et al. recently reported simulations of rare causal variants that lead to association signals of common, tag single nucleotide polymorphisms, dubbed "synthetic associations". However, an open question is what practical implications synthetic associations have for GWAS. Here, we explore the signatures exhibited by such "synthetic associations" and their implications based on patterns of genetic variation observed in human populations, thus accounting for human evolutionary history -a force disregarded in previous simulation studies. This is made possible by human population genetic data from HapMap 3 consisting of both resequencing and array-based genotyping data for the same set of individuals from multiple populations. We report that synthetic associations tend to be further away from the underlying risk alleles compared to "natural associations" (i.e. associations due to underlying common causal variants), but to a much lesser extent than previously predicted, with both the age and the effect size of the risk allele playing a part in this phenomenon. We find that while a synthetic association has a lower probability of capturing causal variants within its linkage disequilibrium block, sequencing around the associated variant need not extend substantially to have a high probability of capturing at least one causal variant. We also show that the minor allele frequency of synthetic associations is lower than of natural associations for most, but not all, loci that we explored. Finally, we find the variance in associated allele frequency to be a potential indicator of synthetic associations.     

Stability of a Lac repressor mediated "looped complex"

The quantitation of the stability of a protein-mediated "looped complex" of the Lac repressor and DNA containing two protein-binding sites whose centers of symmetry are separated by 11 helical turns (114 bp) was accomplished by footprint and gel mobility-shift titration techniques. Lac repressor binding to this DNA was only moderately cooperative; a cooperative free energy of -1.0 kcal/mol was calculated in a model-independent fashion from the individual-site loading energies obtained from the footprint titration studies. In order to partition the cooperative binding energy into components representing the dimer-tetramer association of Lac repressor and the cyclization probability of the intervening DNA, advantage was taken of the presence of experimental measures that were in proportion to the concentration of the looped complex present in solution. One measure was the DNase I hypersensitivity observed in footprint titrations in bands located between the two binding sites. The second measure resulted from the electrophoretic resolution in the gel mobility-shift titrations of the band representing the doubly liganded "tandem complex" from the band representing the singly liganded complexes, including the looped complex. Analysis of the footprint and mobility-shift titration data utilizing this additional information showed that approximately 65% of the molecules present in solution are looped complexes at pH 7.0, 100 mM KCl, and 20 degrees C when the binding sites on the DNA are saturated with protein. Reconciliation of the observed low binding cooperativity and the high proportion of looped complexes could only be obtained when the titration data were analyzed by a model in which Lac repressor tetramers dissociate into dimers in solution. The proportion of looped complexes present in solution is highly dependent on the dimer-tetramer association constant, delta Gtet. This result is consistent with the determination by high-pressure fluorescence techniques that Lac repressor tetramers dissociate with an association free energy comparable to their DNA-binding free energies [Royer, C. A., Chakerian, A. E., & Matthews, K. S. (1990) Biochemistry 29, 4959-4966]. However, when the value of delta Gtet of -10.6 kcal/mol (at 20 degrees C) reported by Royer et al. (1990) is assumed, the titration data demand that tetramers bind DNA with much greater affinity than dimers: a result inconsistent with the destabilization of tetramers by the operator observed in the dimer-tetramer dissociation studies.(ABSTRACT TRUNCATED AT 400 WORDS)     

Diving through the "-omics": the case for deep phenotyping and systems epidemiology

Enabled by diverse high-throughput technologies, the rapidly evolving field of "-omics sciences" offers the potential to study health and disease in breadth and depth at the human population level. We have recently linked genomics and metabolomics to present the first genome-wide association study of metabolic traits in human urine providing new insights into the functional background of chronic kidney disease. We propose systems epidemiology as a novel approach to study the complexities of human pathophysiology by integrating various population-level omic-metrics and to identify new trans-omic biomarkers.     

Physiological and biochemical properties of the bacterial association of <Emphasis Type="Italic">Klebsiella terrigena</Emphasis> E6 and <Emphasis Type="Italic">Bacillus firmus</Emphasis> E3

Physiological and biochemical properties of the natural rhizospheric association of Klebsiella terrigena E6 and Bacillus firmus E3 were studied. It was demonstrated that this association fixed actively molecular nitrogen at a rate of 110 nmol ethylene per 1 mg protein per h. The dynamics of bacterial population in the association and in pure cultures were studied. The properties of this association depended on the ratio of its components; the maximal nitrogen fixation was recorded at a content of B. firmus E310 amounting to 15% of the total cell number. It was demonstrated that the stability basis of this association was the specific interactions via its components via metabolites—phenol and para-hydroxybenzoic acid—as well as via nitrogen fixation, respiration, and pH of the medium. A scheme of the interactions between the components of association is shown.     

"Chromatomics" the analysis of the chromatome

Chromatin is a highly complex mixture of proteins and DNA that is involved in the regulation and coordination of gene expression within the eukaryotic nucleus. Changes in chromatin structure can convey heritable changes of gene activity in response to external stimuli without altering the primary DNA sequence. This epigenetic inheritance of particular traits very likely plays a major role during evolutionary processes. It is however, still ill-defined how this non DNA-mediated inheritance is accomplished at a molecular level. The advent of new methods to systematically study genome-wide changes in chromatin condensation, DNA methylation levels, RNA synthesis and the association of specific proteins or protein modifications now allows a thorough investigation of changes in chromatin structure and function in response to environmental alterations. We would like to review some of these global approaches and to introduce the term "chromatomics" for the systematic analysis of the DNA, RNA and protein content of the genetic material in the eukaryotic nucleus.     

Genetic diversity of Porphyromonas gingivalis isolates recovered from single "refractory" periodontitis sites

Multilocus sequence typing and fimA genotyping were performed on Porphyromonas gingivalis isolates from 15 subjects with "refractory" periodontitis. Several sequence types were detected for most individual pockets. The variation indicated recombination at the recA and pepO genes. The prevalence of fimA genotypes II and IV confirmed their association with periodontitis.     

Characteristic features of the ranks genus and subgenus, and an intercalary rank "species complex" in ixodid ticks (Acari: Ixodidae)

The work was carries our from the standpoint of the morphological conception of species. Vast collections of the Zoological Institute of the Russian Academy of Science testify to the existence of hiatuses in both genera and subgenera of Palearctic ixodids at all active phases of their ontogenesis. The fact that the subgenera of Palearctic genera have been well studies is notes, and composition of the subgenera is presented. The question of a taxonomic intercalary rank "species complex" is considered in detail in the context of the coevolution between some complexes of closely related species of ixodid ticks and some closely related species (genospecies, strains) of pathogens. The question of the taxonomic rank "species complex" in ixodid ticks as a phyletic species association is postulated on the basis of comparative ontogenetic data. Nomenclature status of the intercalary association "species complex" is specified in conformity with the fourth edition of the International Code of Zoological Nomenclature. Species composition of most studied complexes is presented. Some variants of morphological differentiation between species complexes within subgenus are considered. Significance of the taxonomic concept "species complex" for zoological. parasitological, and medical aspects of the ixodid ticks study was evaluated. Prognostic significance of the rank "species complex" for the study of the relationships between ixodid ticks and pathogens is discussed.     

The first report of a putative "entomoparasitic adult form" in Bursaphelenchus

A putative "entomoparasitic adult form" of Bursaphelenchus luxuriosae was found in the tracheal system and body cavity of its cerambycid vector beetle, Acalolepta luxuriosa. Morphologically, this form is intermediate between the usual mycophagous adult and the phoretic dauer juvenile, i.e., it shares the primary and secondary reproductive features with the mycophagous phase but shares a degenerate digestive tract with JIV dauer juveniles. In addition, the "parasitic form" has specialized characters relative to the mycophagous phase analogous to dicyclic Hexatylina, e.g., vacuole-like dots (assumed to be sensory organs) at the anterior end, a very long vulval flap, conical female tail, and elongated male spicules. The presence of insect-parasitic juveniles has been reported in several Bursaphelenchus species, but this is the first confirmed report of a putative "entomoparasitic adult form" in the genus. Thus, the "parasitic adult form" of B. luxuriosae is hypothesized to be an autapomorphic character of this species in the genus. The physiological impact of the parasitism on the host beetle is assumed to be weak because no clear symptoms were observed in the infested beetles. Also, no nematode eggs or propagative juveniles were observed in the beetle host, suggesting that more research is needed to confirm the nature of the association (parasitic vs. endophoretic).     

Prenatal development of "synaptic" ribbons in the guinea pig pineal gland

Pineal "synaptic" ribbons are a heterogeneous population of organelles. "Synaptic" ribbons (SR) sensu stricto, "synaptic" spherules (SS), and intermediate forms (IMF) are present. Their function and origin are unknown, and a knowledge of their prenatal development is lacking. Thus the pineal glands of prenatal, neonatal, and adult guinea pigs were prepared for electron microscopy. "Synaptic" ribbons were studied morphologically and quantitatively. The three categories of "synaptic" ribbons reported in adult pineal glands were also present in prenatal pineal glands. Their structural features, distribution, grouping, and composition patterns are similar to those in adults. "Synaptic" ribbons were first detected in pinealocytes of the distal region of a 42-day postcoitus (PC) pineal gland and were comparable with those in adults. They increased in number with age and reached a peak at 63 days PC, followed by a steep decline at 66 and 67 days PC. By day 69 PC, the numbers increased again and showed a dramatic increase after birth. Several true ribbon synapses were seen at day 63 PC between pinealocyte cell processes or between pinealocyte cell process and pinealocyte cell body. Since true ribbon synapses have not been found in adult guinea pig pinealocytes, their synaptic nature could have been lost during development. No precursors for the "synaptic" ribbons were found. The endoplasmic reticulum cisternae may be the origin for the ribbon vesicles because of their close association with the "synaptic" ribbons.     

Meta-analysis suggests choosy females get sexy sons more than "good genes"

Female preferences for specific male phenotypes have been documented across a wide range of animal taxa, including numerous species where males contribute only gametes to offspring production. Yet, selective pressures maintaining such preferences are among the major unknowns of evolutionary biology. Theoretical studies suggest that preferences can evolve if they confer genetic benefits in terms of increased attractiveness of sons ("Fisherian" models) or overall fitness of offspring ("good genes" models). These two types of models predict, respectively, that male attractiveness is heritable and genetically correlated with fitness. In this meta-analysis, we draw general conclusions from over two decades worth of empirical studies testing these predictions (90 studies on 55 species in total). We found evidence for heritability of male attractiveness. However, attractiveness showed no association with traits directly associated with fitness (life-history traits). Interestingly, it did show a positive correlation with physiological traits, which include immunocompetence and condition. In conclusion, our results support "Fisherian" models of preference evolution, while providing equivocal evidence for "good genes." We pinpoint research directions that should stimulate progress in our understanding of the evolution of female choice.     

Vear, a novel Golgi-associated protein with VHS and gamma-adaptin "ear" domains

The molecular basis of the selectivity and the details of the vesicle formation in endocytic and secretory pathways are still poorly known and most probably involve as yet unidentified components. Here we describe the cloning, expression, and tissue and cell distribution of a novel protein of 67 kDa (called Vear) that bears homology to several endocytosis-associated proteins in that it has a VHS domain in its N terminus. It is also similar to gamma-adaptin, the heavy subunit of AP-1, in having in its C terminus a typical "ear" domain. In immunofluorescence microscopy, Vear was seen in the Golgi complex as judged by a typical distribution pattern, a distinct colocalization with the Golgi marker gamma-adaptin, and a sensitivity to treatment of cells with brefeldin A. In cell fractionation, Vear partitioned with the post-nuclear membrane fraction. In transfection experiments, hemagglutinin-tagged full-length Vear and truncated Vear lacking the VHS domain assembled on and caused compaction of the Golgi complex. Golgi association without compaction was seen with the ear domain of Vear, whereas the VHS domain alone showed a diffuse membrane- and vesicle-associated distribution. The Golgi association and the bipartite structure along with the differential targeting of its domains suggest that Vear is involved in heterotypic vesicle/suborganelle interactions associated with the Golgi complex. Tissue-specific function of Vear is suggested by its high level of expression in kidney, muscle, and heart.     

<Emphasis Type="Italic">PPARGC1B</Emphasis> gene is associated with Kashin-Beck disease in Han Chinese

Kashin-Beck disease (KBD) is a chronic osteochondropathy. The genetic basis of KBD remains elusive now. To investigate the relationship between PPARGC1B gene polymorphism and KBD, we conducted a two-stage association study using 2743 unrelated Han Chinese subjects. In the first stage, three SNPs rs1078324, rs4705372, and rs11743128 of PPARGC1B gene were genotyped in 559 KBD patients and 467 health controls using Sequenom MassARRAY platform. In the second stage, the association analysis results of PPARGC1B with KBD were replicated using an independent sample of 1717 subjects. SNP association analysis was conducted by PLINK software. Genotype imputation was conducted by IMPUTE 2.0 against the reference panel of the 1000 genome project. Bonferroni multiple testing correction was performed. We observed a significant association signal at rs4705372 (P?=?0.0160) and a suggestive association signal at rs11743128 (P?=?0.0290). Further replication study confirmed the association signals of rs4705372 (P?=?0.0026) and rs11743128 (P?=?0.0387) in the independent validation sample. Our study results suggest that PPARGC1B is a novel susceptibility gene of KBD.     

Hans Driesch and the problems of "normal psychology". Rereading his Crisis in Psychology (1925)

In 1925, the German biologist and philosopher Hans Driesch published a booklet entitled The Crisis in Psychology. It was originally published in English and was based on lectures given at various universities in China, Japan and the USA. The "crisis" in psychology of that time, in Driesch's opinion, lies in the necessity to decide about "the road which psychology is to follow in the future". This necessity refers to five "critical points", namely (1) to develop the theory of psychic elements to a theory of meaning by phenomenological analysis, (2) the overcoming of association theory, (3) to acknowledge that the unconscious is a fact and a "normal" aspect of mental life, (4) to reject "psychomechanical parallelism" or any other epiphenomenalistic solution of the mind-body problem, and (5) the extension of psychical research to new facts as described by parapsychology, for instance. Driesch saw close parallels between the development of modern psychology and that of biology, namely in a theoretical shift from "sum-concepts" like association and mechanics, to "totality-concepts" like soul and entelechy. The German translation of 1926 was entitled Grundprobleme der Psychologie (Fundamental Problems of Psychology) while "the crisis in psychology" forms just the subtitle of this book. This underlines that Driesch's argumentation--in contrast to that of Buehler--dealt with ontological questions rather than with paradigms.     

"In situ" characterization of guanine nucleotide-binding properties of erythrocyte membranes

Unsealed membranes from human erythrocytes bind GTP and GTP analogs according to first order kinetics, a single rate constant being observed. With [35S]GTP gamma S this is 0.15 +/- 0.2 min-1. Treatment of the membranes with detergents decreases binding considerably. Scatchard plots reveal uncomplicated patterns of ligand association, with Kd values of 10.2 +/- 2.3 nM [35S]GTP gamma S, of 18.2 +/- 4.3 nM [alpha-32P]GTP and of 28.6 +/- 3.5 nM [alpha-32P]GDP, respectively. The stoichiometry with the three ligands is strictly comparable, i.e. 65 +/- 7 picomoles/mg of membrane protein. Binding of each labeled nucleotide is competitively inhibited by the other two unlabeled ligands, the inhibition constants being very close to the corresponding Kd values. Metabolic depletion and subsequent repletion of intact erythrocytes result in membrane preparations still active in guanine nucleotide binding, with unmodified Kd values. However, the stoichiometry falls to 35 picomoles/mg protein with the "depleted" erythrocyte membranes and regains higher values (50 picomoles/mg protein) with the "repleted" cell membranes. Accordingly, the "in situ" characterization of guanine nucleotide-binding properties of erythrocyte membranes seems to represent a new tool for monitoring the metabolic state of intact erythrocytes.     

The impact of multifunctional genes on "guilt by association" analysis

Many previous studies have shown that by using variants of "guilt-by-association", gene function predictions can be made with very high statistical confidence. In these studies, it is assumed that the "associations" in the data (e.g., protein interaction partners) of a gene are necessary in establishing "guilt". In this paper we show that multifunctionality, rather than association, is a primary driver of gene function prediction. We first show that knowledge of the degree of multifunctionality alone can produce astonishingly strong performance when used as a predictor of gene function. We then demonstrate how multifunctionality is encoded in gene interaction data (such as protein interactions and coexpression networks) and how this can feed forward into gene function prediction algorithms. We find that high-quality gene function predictions can be made using data that possesses no information on which gene interacts with which. By examining a wide range of networks from mouse, human and yeast, as well as multiple prediction methods and evaluation metrics, we provide evidence that this problem is pervasive and does not reflect the failings of any particular algorithm or data type. We propose computational controls that can be used to provide more meaningful control when estimating gene function prediction performance. We suggest that this source of bias due to multifunctionality is important to control for, with widespread implications for the interpretation of genomics studies.     

Field associations of first generation densities of the pest mites <Emphasis Type="Italic">Halotydeus destructor</Emphasis> and <Emphasis Type="Italic">Penthaleus major</Emphasis> in pasture

Halotydeus destructor and Penthaleus major are species of earth mite commonly found at high densities in agricultural fields in Australia and other parts of the world. These mites pose a risk to a range of winter crops and pastures when seedlings emerge in autumn. In order to predict likely mite pressure, we investigated whether autumn densities in pastures can be determined from agronomic and environmental field variables. For H. destructor, field densities showed little association with a range of vegetation variables but could largely be explained using the variable field type, with high densities present when fields had mixtures of grass, clover and weeds. For P. major, we found a regional effect. In the region where most data were available, P. major field densities were associated with grass abundance, whereas an association with field type was significant but different to that found for H. destructor. For both species, densities were not associated with rainfall, but there was a weak association with soil moisture capacity. We discuss how these results can help in managing these important pest mites.     

High affinity RNase S-peptide variants obtained by phage display have a novel "hot-spot" of binding energy.

Using phage display mutagenesis, high affinity variants of RNase S-peptide were produced that bind to RNase S-protein over 100-fold more tightly than the wild type S-peptide. The S-peptide: S-protein interface was further characterized using "biased" phage display libraries, where each targeted residue was constrained to be either polar or nonpolar. The use of these tailored libraries placed constraints on the type of interactions present during affinity maturation process and allowed more amino acids to be randomized simultaneously. These results, in conjunction with kinetic association and dissociation constants determined by surface plasmon resonance (SPR), highlight the role of a single mutation (A5W) in increasing S-peptide binding affinity. High affinity S-peptide variants were only identified when tryptophan was present in the phage display library at position 5, suggesting that this residue is a "hot-spot" of binding energy in the high affinity variants. Analysis of SPR data in the presence of denaturant suggests that the increased affinity is a result of increased hydrophobic interactions in the transition state rather than a stabilization of helical structure.