Linking the branchpoint helix to a newly found receptor allows lariat formation by a group II intron

Like spliceosomal introns, the ribozyme-containing group II introns are excised as branched, lariat structures: a 2'-5' bond is created between the first nucleotide of the intron and an adenosine in domain VI, a component which is missing from available crystal structures of the ribozyme. Comparative sequence analysis, modelling and nucleotide substitutions point to the existence, and probable location, of a specific RNA receptor for the section of domain VI that lies just distal to the branchpoint adenosine. By designing oligonucleotides that tether domain VI to this novel binding site, we have been able to specifically activate lariat formation in an engineered, defective group II ribozyme. The location of the newly identified receptor implies that prior to exon ligation, the distal part of domain VI undergoes a major translocation, which can now be brought under control by the system of anchoring oligonucleotides we have developed. Interestingly, these oligonucleotides, which link the branchpoint helix and the binding site for intron nucleotides 3-4, may be viewed as counterparts of U2-U6 helix III in the spliceosome.     

Intra-individual coexistence of a Wolbachia strain required for host oogenesis with two strains inducing cytoplasmic incompatibility in the wasp Asobara tabida

Cytoplasmically inherited symbiotic Wolbachia bacteria are known to induce a diversity of phenotypes on their numerous arthropod hosts including cytoplasmic incompatibility, male-killing, thelytokous parthenogenesis, and feminization. In the wasp Asobara tabida (Braconidae), in which all individuals harbor three genotypic Wolbachia strains (wAtab1, wAtab2 and wAtab3), the presence of Wolbachia is required for insect oogenesis. To elucidate the phenotype of each Wolbachia strain on host reproduction, especially on oogenesis, we established lines of A. tabida harboring different combinations of these three bacterial strains. We found that wAtab3 is essential for wasp oogenesis, whereas the two other strains, wAtabl and wAtab2, seem incapable to act on this function. Furthermore, interline crosses showed that strains wAtab1 and wAtab2 induce partial (about 78%) cytoplasmic incompatibility of the female mortality type. These results support the idea that bacterial genotype is a major factor determining the phenotype induced by Wolbachia on A. tabida hosts. We discuss the implications of these findings for current hypotheses regarding the evolutionary mechanisms by which females of A. tabida have become dependent on Wolbachia for oogenesis.     

Detection of biomolecular interaction between biotin and streptavidin on a self-assembled monolayer using magnetic nanoparticles

For developing a magnetic bioassay system, an investigation to determine the presence of a specific biomolecular interaction between biotin and streptavidin was done using magnetic nanoparticles and a silicon substrate with a self-assembled monolayer. Streptavidin was immobilized on the magnetic particles, and biotin was attached to the monolayer-modified substrate. The reaction of streptavidin-modified magnetic particles on the biotin-modified substrate was clearly observed under an optical microscope. The magnetic signals from the particles were detected using a magnetic force microscope. The results of this study demonstrate that the combination of a monolayer-modified substrate with biomolecule-modified magnetic particles is useful for detecting biomolecular interactions in medical and diagnostic analyses.     

Calix[8]arene-mediated self-assembly of tetrapeptide H-Leu-Leu-Ile-Leu-OMe

Conformational analysis of peptide 1, H-Leu-Leu-Ile-Leu-OMe on complexing with macro cycle calix[8]arene has been carried out using (1)H-NMR and FTIR spectroscopic techniques. Stoichiometry of the complex formed in the 1:8 ratio was evidenced by a Job plot. NMR studies of the above peptide show a marked downfield shift and an increase in (3)J values for NH resonances on complexing with calix[8]arene. The characteristic NOE connectivity between N(i+1)H and C(ialpha)H confirm beta-sheet conformation in the complexed state. Both (1)H-NMR and FTIR results indicate that the alpha-amino group of Leu I is proximal to the macrocycle and is involved in hydrogen bond formation with phenolic hydrogen atom of the calix[8]arene. This suggests that calix[8]arene provides a suitable platform for peptide 1 to self-assemble in a parallel beta-sheet conformation. The nature of calix[8]arene interaction with peptide 1 has been studied using dynamic NMR studies, which concludes that a bifurcated hydrogen bonding interaction exists in the molecular interfaces of the assembly.     

DNA condensation by high-affinity interaction with avidin

Avidin, the basic biotin-binding glycoprotein from chicken egg white, is known to interact with DNA, whereas streptavidin, its neutral non-glycosylated bacterial analog, does not. In the present study we investigated the DNA-binding properties of avidin. Its affinity for DNA in the presence and absence of biotin was compared with that of other positively charged molecules, namely the protein lysozyme, the cationic polymers polylysine and polyarginine and an avidin derivative with higher isoelectric point (pI approximately 11) in which most of the lysine residues were converted to homoarginines. Gel-shift assays, transmission electron microscopy and dynamic light scattering experiments demonstrated an unexpectedly strong interaction between avidin and DNA. The most pronounced gel-shift retardation occurred with the avidin-biotin complex, followed by avidin alone and then guanidylated avidin. Furthermore, ultrastructural and light-scattering studies showed that avidin assembles on the DNA molecule in an organized manner. The assembly leads to the formation of nanoparticles that are about 50-100 nm in size (DNA approximately 5 kb) and have a rod-like or toroidal shape. In these particles the DNA is highly condensed and one avidin is bound to each 18 +/- 4 DNA base pairs. The complexes are very stable even at high dilution ([DNA] =10 pM) and are not disrupted in the presence of buffers or salt (up to 200 mM NaCl). The other positively charged molecules also condense DNA and form particles with a globular shape. However, in this case, these particles disassemble by dilution or in the presence of low salt concentration. The results indicate that the interaction of avidin with DNA may also occur under physiological conditions, further enhanced by the presence of biotin. This DNA-binding property of avidin may thus shed light on a potentially new physiological role for the protein in its natural environment.     

Spore killing in the fungus Podospora anserina: a connection between meiotic drive and vegetative incompatibility?

Fungi in which the haploid nuclei resulting from meiosis are linearly arranged in asci provide unique opportunities to analyse abnormal segregation. Any meiotic drive system in such fungi will be observed in a cross between a driving and a sensitive strain as spore killing: the degeneration of half the ascospores in a certain proportion of the asci. In a sample of some 100 strains isolated from a single natural population we have discovered at least six different meiotic drive elements (van der Gaag et al., 2000). Here we report results of research that was aimed at elucidating a possible correlation between meiotic drive and vegetative incompatibility in eight different Spore killer strains from this population. We show that there is a strong correlation between these two phenotypes, although the precise genetic nature of the correlation is not yet clear. We discuss the implications of our results for the understanding of the population genetics of meiotic drive in Podospora.     

G-quartet self-assembly under osmotic pressure: remote control by vesicle shrinking rather than stress

Does osmotic pressure stimulate assembly or disassembly of supramolecules in vesicles? Self‐assembly was conceivable as intravesicular response to osmotic shrinking upon application of extravesicular overpressure, whereas disassembly was conceivable as a response to bilayer stress in hyperosmotic vesicles. Self‐assembly of guanosine 5′‐monophosphates (GMPs) into G‐quartets was selected to investigate the nature of remote control of supramolecular chemistry within vesicles by osmotic pressure. Using circular dichroism spectroscopy to selectively detect G‐quartets, we found that extravesicular overpressure stimulates intravesicular self‐assembly, whereas underpressure stimulates disassembly. G‐quartet self‐assembly by osmotic pressure exhibited ion‐selective metal‐cation templation, as expected. The key conclusions are that supramolecular chemistry within vesicles is governed by vesicle shape rather than vesicle stress and that detection of osmotic pressure by CD spectroscopy is an interesting alternative to the commonly used methods based on fluorescence self‐quenching. Chirality 15:766–771, 2003. © 2003 Wiley‐Liss, Inc.     

On the logical relationship between natural selection and self-organization

Most evolutionary biologists cherish Darwin's theory of natural selection (NS) as the process of adaptive evolution more than 140 years after publication of his first book on the subject. However, in the past few decades the study of self-organization (SO) in complex dynamical systems has suggested that adaptation may occur through intrinsic reorganization without NS. In this study, we attempt to describe the logical framework that relates the general process of SO to the specific process of NS. We describe NS as a mechanism that coordinates the coevolution of species in an ecosystem to effectively capture, process and dissipate solar energy into the earth's shadow. Finally, we conclude that NS is an emergent process founded on the same thermodynamic imperatives that are thought to underlie all SO. This perspective suggests that the theory of self-organizing systems offers a broader physical context in which to understand the process of NS, rather than contesting it. It even suggests the possibility that there may be a physical basis for understanding the origin of the process of NS. Rather than being merely a fluke of nature, the origin of NS that may be driven by energy flows across gradients.     

Correlates of BMI misreporting among apparently healthy individuals: the ATTICA study

Objective: The aim of this study was to investigate correlates of misreporting in BMI, based on self‐reported weight and height, in a randomly selected population sample of Greek adults and to evaluate the effect of obesity status misclassification on the associations between obesity and disease. Research Methods and Procedures: During 2001 to 2002, we randomly enrolled 1514 men (18 to 87 years old) and 1528 women (18 to 89 years old) from the Attica area, Greece; the sampling was stratified by the age‐sex distribution of the region. Various sociodemographic, clinical, and psychological characteristics were self‐reported, and weight and height were measured and recorded in all participants. Results: The proportions of true positives and true negatives for correct obesity status identification were 62% and 97%, respectively. Women were 9 times more likely to be under‐reporters than men, whereas men were 7.5 times more likely to be over‐reporters. A 10‐year increase in age was associated with a 48% higher likelihood of being an under‐reporter and 26% lower likelihood of being an over‐reporter, irrespective of sex and other characteristics of the participants. Clinical status, such as the presence of hypertension and diabetes, was associated with under‐reporting of body weight. Furthermore, the use of self‐reported data may substantially exaggerate associations between obesity and obesity‐related diseases, such as diabetes, hypercholesterolemia, and hypertension. Discussion: The study indicates that, apart from age and sex, disease status may be another factor that influences misreporting of obesity status, with diabetic and hypertensive people to be more likely to under‐report their overweight. Use of self‐reported data may bias obesity—disease associations.