Protein-RNA interactions: a structural analysis

A detailed computational analysis of 32 protein–RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein–double-stranded DNA and protein–single-stranded DNA complexes. The interface properties of the protein–RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein–RNA and protein–DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein–RNA complexes, backbone contacts were more dominant in the protein–DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.     

Mechanochemical regulation of oscillatory follicle cell dynamics in the developing Drosophila egg chamber

During tissue elongation from stage 9 to stage 10 in Drosophila oogenesis, the egg chamber increases in length by ∼1.7-fold while increasing in volume by eightfold. During these stages, spontaneous oscillations in the contraction of cell basal surfaces develop in a subset of follicle cells. This patterned activity is required for elongation of the egg chamber; however, the mechanisms generating the spatiotemporal pattern have been unclear. Here we use a combination of quantitative modeling and experimental perturbation to show that mechanochemical interactions are sufficient to generate oscillations of myosin contractile activity in the observed spatiotemporal pattern. We propose that follicle cells in the epithelial layer contract against pressure in the expanding egg chamber. As tension in the epithelial layer increases, Rho kinase signaling activates myosin assembly and contraction. The activation process is cooperative, leading to a limit cycle in the myosin dynamics. Our model produces asynchronous oscillations in follicle cell area and myosin content, consistent with experimental observations. In addition, we test the prediction that removal of the basal lamina will increase the average oscillation period. The model demonstrates that in principle, mechanochemical interactions are sufficient to drive patterning and morphogenesis, independent of patterned gene expression.     

Male contributions to egg production: the role of accessory gland products and sperm in Drosophila melanogaster

Drosophila melanogatser seminal fluid components, accessory gland proteins (Acps) and sperm, induce females to deposit high numbers of fertilized eggs for about 11 days. This high and sustained level of egg deposition requires that oogenesis be stimulated to provide the necessary mature oocytes. To investigate the relative timing and contributions of Acps and sperm in the egg-production process, we examined the rates of oogenic progression and egg deposition in females mated to genetically altered males that have seminal fluid deficient in Acps and/or sperm, and subjected these data to path analysis. We found that Acps and sperm are complementary stimuli necessary for inducing high rates of oogenic progression and rapid egg deposition. While egg deposition and oogenic progression can be induced by Acps alone, both Acps and sperm are required for maximum stimulation of oogenic progression and egg deposition immediately after mating.     

A structural analysis of G-quadruplex/ligand interactions

This focused review article discusses in detail, all available high-resolution small molecule ligand/G-quadruplex structural data derived from crystallographic and NMR based techniques, in an attempt to understand key factors in ligand binding and to highlight the biological importance of these complexes. In contrast to duplex DNA, G-quadruplexes are four-stranded nucleic acid structures folded from guanine rich repeat sequences stabilized by the stacking of guanine G-quartets and extensive Watson-Crick/Hoogsteen hydrogen bonding. Thermally stable, these topologies can play a role in telomere regulation and gene expression. The core structures of G-quadruplexes form stable scaffolds while the loops have been shown, by the addition of small molecule ligands, to be sufficiently adaptable to generate new and extended binding platforms for ligands to associate, either by extending G-quartet surfaces or by forming additional planar dinucleotide pairings. Many of these structurally characterised loop rearrangements were totally unexpected opening up new opportunities for the design of selective ligands. However these rearrangements do significantly complicate attempts to rationally design ligands against well defined but unbound topologies, as seen for the series of napthalene diimides complexes. Drawing together previous findings and with the introduction of two new crystallographic quadruplex/ligand structures we aim to expand the understanding of possible structural adaptations available to quadruplexes in the presence of ligands, thereby aiding in the design of new selective entities.     

Studies on the interactions of sperm with the surface of the sea urchin egg

We have examined the relationship between sperm adhesion and fertilization in the cross species insemination of Arbacia punctulata eggs by Strongylocentrotus purpuratus sperm. As previously reported (Kinsey et al., 1980) the addition of S. purpuratus egg jelly results in induction of the acrosome reaction in sperm and significant numbers of S. purpuratus sperm adhere to A. punctulata eggs. However, in the absence of S. purpuratus egg jelly, S. purpuratus sperm fail to bind to A. punctulata eggs. Although at least 200 S. purpuratus sperm bind to an A. punctulata egg in the presence of S. purpuratus jelly, less than 8% of the eggs are fertilized. The adhesion of S. purpuratus sperm meets the same functional criteria as homologous A. punctulata sperm-egg adhesion. Electron microscopy shows that S. purpuratus sperm that have undergone the acrosome reaction adhere to A. punctulata eggs by their bindin-coated acrosomal process in a manner that is morphologically identical to that observed with homologous A. punctulata sperm. We have also compared the ability of S. purpuratus and A. punctulata sperm to fuse and fertilize with A. punctulata eggs after removal of the vitelline layer. Using high levels of sperm of either species, heterologous as well as homologous fertilization is readily detectable. Under these conditions, where stable binding is not demonstrable, there is no difference in the ability of S. purpuratus and A. punctulata sperm to fertilize A. punctulata eggs. These observations suggest that the failure of S. purpuratus sperm to fertilize A. punctulata eggs under normal conditions may be due to their inability to penetrate the vitelline layer so that they can fuse with the egg plasma membrane. In relation to the possible mechanism of vitelline layer penetration, we have also investigated the mode of action of chymostatin, an inhibitor of chymotrypsin that has been reported to inhibit fertilization of sea urchin eggs (Hoshi et al., 1979). Our findings suggest that the fertilization inhibitory activity of chymostatin is not related to its antichymotrypsin activity. Rather, it appears that this inhibition is due to the induction of an abnormal acrosome reaction in sperm that precludes formation of the acrosome process.     

Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data

Background  

Over the past decade our laboratory has focused on understanding how soluble cytoskeleton-associated proteins interact with membranes and other lipid aggregates. Many protein domains mediating specific cell membrane interactions appear by fluorescence microscopy and other precision techniques to be partially inserted into the lipid bilayer. It is unclear whether these protein-lipid-interactions are dependent on shared protein motifs or unique regional physiochemistry, or are due to more global characteristics of the protein.     

Interspecific analysis of the glycosidases of the sperm plasma membrane in Drosophila

We have studied the presence of four sperm glycosidases, alpha-mannosidase, alpha-L- fucosidase and two beta-hexosaminidase isoforms, in 11 species of the genus Drosophila spanning approximately an evolutionary 60 MY period, and in Scaptodrosophila lebanonensis, belonging to the ancestor genus Scaptodrosophila. These enzymes had been previously identified in Drosophila melanogaster as putative receptors for glycoconjugates of the egg surface. Alpha-mannosidase and beta-hexosaminidases are intrinsic proteins of the sperm plasma membrane in species closely related to D. melanogaster as well as in the divergent species D. willistoni, D. hydei, D. virilis, and S. lebanonensis. Alpha-L-fucosidase is restricted to the species of the genus Drosophila. Alpha-mannosidase and beta-hexosaminidases have been purified and characterized in all species. Their molecular masses and optimal pHs are similar in all the species, whereas interspecific differences in enzyme activities were detected. Cross-species comparison of kinetic parameters indicated a relationship between enzyme efficiency and phylogenetic relatedness. Beta-hexosaminidases were the most efficient enzymes. Lectin cytochemistry suggested the presence of carbohydrate residues complementary to the glycosidases on the eggshell at the site of sperm entry in all species. Bioinformatic analysis of the coding sequences of beta-hexosaminases and alpha-L-fucosidase and of their predicted products showed no evidence of positive selection of the genes coding for these enzymes and a high degree of sequence identity of the predicted polypeptides among the species of the genus Drosophila. Collectively, our findings indicate that the Drosophila sperm glycosidases are structurally and functionally conserved and strengthen the hypothesis of their involvement in the interactions with the egg surface.     

Adaptation to long sperm in Drosophila: correlated development of the sperm roller and sperm packaging

Sperm are generally small and produced in huge numbers, but some species combine exaggerated sperm length with extremely limited numbers of sperm, an evolutionary trend that deviates from the theory of anisogamy. Sperm gigantism has arisen recurrently in various species, but insects exhibit the longest sperm, with some species of the Drosophilidae family producing sperm up to 6 cm in length. The anatomical, cytological, and physiological requirements for males to cope with these giant sperm were hitherto poorly understood. In this paper, we investigate the internal morphology of the male reproductive tract, and highlight specific features that may be linked to this increase in sperm size. We focus on species in the repleta group, within which sperm length varies by a factor of 35. An associated development of the sperm roller, a special twisting device inserted between the testis and the seminal vesicle, is demonstrated. Its length and the number of coils involved increase with sperm size, and it allows individual sperm to swell and roll into a spermatic pellet before reaching the seminal vesicle. This process occurs independently of and in addition to the sperm bundle coiling that takes place at the base of the testis. It is suggested that the emergence and development of the sperm roller may be a male adaptation to sperm gigantism.     

Surface interactions between mammalian sperm and egg: variation of spermatozoa concentration as a probe for the study of binding in vitro.

The pre-penetration binding interactions between gametes of the golden hamster were investigated in vitro. Binding between capacitated spermatozoa and the surface of eggs, that is the zonae pellucidae with intact vitelli, as a function of the concentration of spermatozoa, followed a sigmoidal curve. This was in sharp contrast to the linear binding obtained with mechanically isolated zonae pellucidae (zonae lacking vitelli). Penetration of eggs as a function of the concentration of spermatozoa paralleled the binding curve that occurred between gametes. The binding curve obtained with uncapacitated spermatozoa and eggs was not sigmoidal but was linear after a slight lag and parallel to the curve obtained with uncapacitated spermatozoa and isolated zonae pellucidae. Taken together these results support previous work which implicated a vitelline factor in the binding reaction between the surfaces of eggs and capacitated spermatozoa. By scoring binding at one minute intervals it was possible to relate the rapid uninterrupted binding that occurs between capacitated spermatozoa and isolated zonae pellucidae with the equally rapid but transient and vitellus-influenced binding that occurs between gametes. It was concluded that the vitelline factor acts by preventing most of the early type of binding that occurs between spermatozoa and isolated zonae pellucidae and not by terminating the early, rapid, initial binding as previously postulated. Thus, this early binding never occurs between most of the gametes that finally bind 30 to 40 minutes later and, therefore, does not play a role in the establishment of the late binding step which leads to penetration.     

Hormonal correlates of human paternal interactions: a hospital-based investigation in urban Jamaica

To expand our understanding of the neuroendocrine mechanisms underlying human fatherhood, including its cross-cultural expression, we investigated the hormonal correlates of fatherhood in the greater Kingston, Jamaica area. We recruited 43 men, aged 18-38, to participate: 15 single men; 16 "coresidential" fathers (men who live with their adult female partner and youngest child); and 12 "visiting" fathers (men who live apart from their adult female partner and youngest child). The research protocol entailed biological sampling before and after a 20-min behavioral session during which single men sat alone and fathers interacted with their partner and youngest child. Hormone measures relied upon minimally invasive techniques (salivary testosterone and cortisol, finger prick blood spot prolactin, urinary oxytocin and vasopressin). Results revealed significant group differences in average male testosterone levels (p=0.006), with post hoc contrasts indicating that visiting fathers had significantly (p<0.05) lower testosterone levels than single men. Prolactin profiles also differed significantly across groups (p=0.010) whereby post hoc contrasts showed that prolactin levels of single men declined significantly compared with the flat levels of visiting fathers (p<0.05). No group differences in cortisol, oxytocin or vasopressin levels were observed. However, among fathers, vasopressin levels were significantly and negatively (r=-.431, p=0.022) correlated with the age of a man's youngest child. These results thus implicate lower testosterone levels as well as prolactin and vasopressin in human fatherhood. These findings also highlight the importance of sociocultural context in human fatherhood while exhibiting parallels with existing data on the non-human vertebrate hormonal bases of paternal care.     

A stereological analysis of developing egg chambers in Ephestia kuhniella

A polytrophic ovariole of the flour moth, Ephestia kuhniella, is composed of a linear series of increasingly mature egg chambers, each consisting of an oocyte, an interconnected cluster of seven nurse cells, and a covering layer of follicle cells. This study describes changes in the volume of each component as a function of the position of the egg chamber in the ovariole. Analysis of the growth curve of the Ephestia oocyte yields two possible correlations between accelerated oocyte growth and ultrastructural events enhancing the supply of yolk materials to the oocyte: the first is the initiation of yolk synthesis by the follicle cell layer and its transfer to the oocyte, and the second is the formation of channels between the follicle cells allowing hemolymph to gain access to the oocyte. An Ephestia oocyte increases in volume from approximately 2.5 × 10³ μm³ to approximately 2.0 × 10⁷ μm³ over an average series of 58 egg chambers.     

Spotting the differences: Probing host/microbiota interactions with a dedicated software tool for the analysis of faecal outputs in Drosophila

The intestinal physiology of Drosophila melanogaster can be monitored in an integrative, non-invasive manner by analysing graphical features of the excreta produced by flies fed on a dye-supplemented diet. This assay has been used by various labs to explore gut function and its regulation. To facilitate its use, we present here a free, stand-alone dedicated software tool for the analysis of fly excreta. The Ultimate Reader of Dung (T.U.R.D.) is designed to offer a flexible environment for a wide range of experimental designs, with special attention to automation and high-throughput processing. This software detects the distinctive changes in acid-base and water balance previously reported to occur in response to dietary challenges and mating. We have used T.U.R.D. to test the contribution of the bacterial environment of the flies to various intestinal parameters including the established diet- and mating-triggered responses. To this end, we have analysed the faecal patterns of flies reared in germ-free conditions, upon re-association with controlled microbiota and subjected to food-borne or systemic, non-lethal bacterial infections. We find that the tested faecal outputs are unchanged in all these conditions, suggesting that the impact of the bacterial environment on the intestinal features highlighted by faecal deposit analysis is minimal.     

An analysis of structural aberrations in human sperm chromosomes

We have analyzed structural aberrations in 5,000 sperm chromosome complements obtained from 20 men over a 5-yr period by fusion of human sperm with hamster eggs. Detailed data are presented on 366 abnormal cells with 379 analyzable breakpoints. The frequency of cells with structural aberrations ranged from 1.9% to 14.5% among donors; this interindividual variability was statistically significant (p less than 0.0001). In contrast, repeat samples from individual men showed no significant variation over time. The number of sperm chromosome sets processed per hamster egg had no effect on the frequency with which structural aberrations occurred, nor were sperm chromosome abnormalities altered by varying capacitation or culture conditions. The spectrum of structural aberrations observed in human sperm chromosomes and a chi-square analysis of breakpoints based on DNA content are presented. Although human sperm chromosome abnormalities were visualized with a cross-species system, we believe that they represent an inherent, biologically significant phenomenon.     

Polarity of sperm entry in the ascidian egg

We have investigated the point of sperm entry in denuded eggs of the ascidian Phallusia mammillata. In contrast to what is generally believed, the sperm show a strong tendency to enter the animal hemisphere rather than the vegetal hemisphere. After entry, the sperm nucleus is carried toward the vegetal pole of the egg during the cortical contraction which occurs within a few minutes after fertilization. This polarity of sperm entry is abolished and the entry point is randomized by pretreating the eggs with cytochalasin D. We suggest that cytochalasin may act by randomizing components needed for sperm attachment or fusion, or structures needed for sperm entry.     

A Drosophila model for genetic analysis of influenza viral/host interactions

Influenza viruses impose a constant threat to vertebrates susceptible to this family of viruses. We have developed a new tool to study virus-host interactions that play key roles in viral replication and to help identify novel anti-influenza drug targets. Via the UAS/Gal4 system we ectopically expressed the influenza virus M2 gene in Drosophila melanogaster and generated dose-sensitive phenotypes in the eye and wing. We have confirmed that the M2 proton channel is properly targeted to cell membranes in Drosophila tissues and functions as a proton channel by altering intracellular pH. As part of the efficacy for potential anti-influenza drug screens, we have also demonstrated that the anti-influenza drug amantadine, which targets the M2 proton channel, suppressed the UAS-M2 mutant phenotype when fed to larvae. In a candidate gene screen we identified mutations in components of the vacuolar V1V0 ATPase that modify the UAS-M2 phenotype. Importantly, in this study we demonstrate that Drosophila genetic interactions translate directly to physiological requirements of the influenza A virus for these components in mammalian cells. Overexpressing specific V1 subunits altered the replication capacity of influenza virus in cell culture and suggests that drugs targeting the enzyme complex via these subunits may be useful in anti-influenza drug therapies. Moreover, this study adds credence to the idea of using the M2 "flu fly" to identify new and previously unconsidered cellular genes as potential drug targets and to provide insight into basic mechanisms of influenza virus biology.     

Intracellular catalase function: analysis of the catalatic activity by product formation in isolated liver cells

Intracellular catalase activity was measured in isolated rat hepatocytes by adding H₂O₂ under anaerobic conditions and measuring O₂ evolution. Hydrogen peroxide was introduced either by continuous infusion or by pulse injection. Continuous infusion at a rate similar to the endogenous H₂O₂ production rate provided results that 60–70% of the H₂O₂ was metabolized by the catalatic reaction. Comparison of rates of O₂ evolution to estimated rates of H₂O₂ metabolism obtained by the methanol-titration method (H. Sies and B. Chance, 1970, FEBS Lett.11, 172–176) indicated that the contribution of the peroxidatic reaction of catalase was small. The intracellular activity of glutathione peroxidase was estimated as the catalase-independent metabolism and used to determine the rate of intracellular H₂O₂ metabolism by the peroxidase. The results provide a quantitative basis for analysis of the physiological and toxicological aspects of H₂O₂ metabolism by liver.