Cytochemical and fine structural analysis of oogenesis in the gastropod, Ilyanassa obsoleta

An analysis of differentiating oocytes of the gastropod, Ilyanassa obsoleta, has been made by techniques of light and electron microscopy. Early previtellogenic oocytes are limited by a smooth surfaced oolemma and are associated with each other by maculae adhaerentes. Previtellogenic oocytes are also distinguished by a large nucleus containing randomly dispersed aggregates of chromatin. Within the ooplasm are Golgi complexes, mitochondria and a few cisternae of the rough endoplasmic reticulum. When vitellogenesis begins, the oolemma becomes morphologically specialized by the formation of microvilli. One also notices an increase in the number of organelles and inclusions such as lipid droplets. During vitellogenesis there is a dilation of the saccules of the Golgi complexes and cisternae of the endoplasmic reticulum. Associated with the Golgi complexes are small protein-carbohydrate yolk precursors encompassed by a membrane. These increase in size by fusing with each other. The “mature” yolk body is a membrane-bounded structure with a central striated core and a granular periphery. At maturity a major portion of the ooplasmic constituents such as as mitochondria and lipid droplets occupy the animal region while the bulk of the population of yolk bodies are situated in the vegetal hemisphere. The follicle cells incompletely encompass the developing oocyte. In addition to the regularly occurring organelles, follicle cells are characterized by the presence of large quantities of rough endoplasmic reticulum and Golgi complexes whose saccules are filled with a dense substance. Associated with the Golgi saccules are secretory droplets of varied size. Amongst the differentiating oocytes and follicle cells are Leydig cells. These cells are characterized by a large vacuole containing glycogen. A possible function for the follicle and Leydig cells is discussed.     

Secretion of predicted Inc proteins of Chlamydia pneumoniae by a heterologous type III machinery

Chlamydia spp. are strictly intracellular pathogens that grow inside a vacuole, called an inclusion. They possess genes encoding proteins homologous to components of type III secretion machineries, which, in other bacterial pathogens, are involved in delivery of bacterial proteins within or through the membrane of eukaryotic host cells. Inc proteins are chlamydial proteins that are associated with the inclusion membrane and are characterized by the presence of a large hydrophobic domain in their amino acid sequence. To investigate whether Inc proteins and other proteins exhibiting a similar hydropathic profile might be secreted by a type III system, we used a heterologous secretion system. Chimeras were constructed by fusing the N-terminal part of these proteins with a reporter, the Cya protein of Bordetella pertussis, and these were expressed in various strains of Shigella flexneri. We demonstrate that these hybrid proteins are secreted by the type III secretion system of S. flexneri, thereby providing evidence that IncA, IncB and IncC are secreted by a type III mechanism in chlamydiae. Moreover, we show that three other proteins from Chlamydia pneumoniae, all of which have in common the presence of a large hydrophobic domain, are also secreted by S. flexneri type III secretion machinery.     

The role of N-glycans in spermatogenesis

Many proteins, in particular those in the plasma membranes, are glycosylated with carbohydrates, which are grouped into O-glycans and N-glycans. O-glycans are synthesized step by step by glycosyltransferases, whereas N-glycans are synthesized by en-bloc transfer of the so-called high-mannose-type oligosaccharide from lipid-linked precursor to polypeptide. The high-mannose-type N-glycans are then modified by processing alpha-mannosidases. Alpha-mannosidase IIx (MX) was identified as the gene product of processing alpha-mannosidase II (MII)-related gene. MX apparently plays subsidiary role for MII in many cell types, as N-glycan patterns of MX null mouse tissues are not altered significantly. Surprisingly MX null male mice are infertile due to a failure of spermatogenesis. This review provides a brief overview of the in vivo role of N-glycans which are revealed by the gene knockout mouse approach, and introduce our studies on the MX gene knockout mouse. The MX gene knockout experiments unveiled a novel function of a specific N-glycan, which is N-acetylglucosamine-terminated and has a fucosylated triantennary structure, in the adhesion between germ cells and Sertoli cells. The study of MX is a good example of how the in vivo roles of an apparently redundant gene product are determined by the gene knockout approach.     

Low resistance junctions in crayfish. Structural changes with functional uncoupling

Electrical uncoupling of crayfish septate lateral giant axons is paralleled by structural changes in the gap junctions. The changes are characterized by a tighter aggregation of the intramembrane particles and a decrease in the overall width of the junction and the thickness of the gap. Preliminary measurements indicate also a decrease in particle diameter. The uncoupling is produced by in vitro treatment of crayfish abdominal cords either with a Ca++, Mg++-free solution containing EDTA, followed by return to normal saline (Van Harreveld's solution), or with VAn Harreveld's solution containing dinitrophenol (DNP). The uncoupling is monitored by the intracellular recording of the electrical resistance at a septum between lateral giant axons. The junctions of the same septum are examined in thin sections; those of other ganglia of the same chain used for the electrical measurements are studied by freeze-fracture. In controls, most junctions contain a more or less regular array of particles repeating at a center to center distance of approximately 200 A. The overall width of the junctions is approximately 200 A and the gap thickness is 40-50 A. Vesicles (400-700 A in diameter) are closely apposed to the junctional membranes. In uncoupled axons, most junctions contain a hexagonal array of particles repeating at a center to center distance of 150-155 A. The overall width of the junctions is approximately 180 A and the gap thickness is 20-30 A. These junctions are usually curved and are rarely associated with vesicles. Isolated, PTA-stained junctions, also believed to be uncoupled, display similar structural features. There are reasons to believe that the changes in structure and permeability are triggered by an increase in the intracellular free Ca++ concentration. Most likely, the changes in permeability are caused by conformational changes in some components of the intramembrane particles at the gap junctions.     

The interactions of enzyme and chemical probes with inverted repeats in supercoiled DNA

In negatively supercoiled DNA molecules some inverted repeat sequences adopt a perturbed conformation which is characterised by the following properties. They are centrally hypersensitive to single-strand-specific nucleases such as S1, and to a much lower extent the flanking regions may also be sensitive. They are also hypersensitive to modification by bromoacetaldehyde, particularly in their flanking region. They may be resistant to endonucleolysis by restriction enzymes and are cleaved (resolved) by a T4 resolving enzyme. All these properties can only be consistently explained by a model in which the inverted repeat adopts a cruciform structure. This property has been shown to depend sharply on a superhelix density, and the transition to nuclease sensitivity is accompanied by a marked alteration in the overall molecular geometry as judged by frictional properties. The probable dynamics of these structures are discussed.     

The Turing-Child energy field as a driver of early mammalian development

The equivalence of the early mammalian cells, of importance in assisted reproductive technologies (ART), is considered. It is suggested that this controversial topic can be settled by finding whether the cells are distinguished by the Turing-Child (TC) field, as expressed for example by patterns of mitochondrial activity. The division of the pronuclear embryo is driven by a symmetrical bipolar TC pattern whose experimental shape and chemical nature is predicted by TC theory. This bipolar pattern drives the subsequent cell divisions too, and according to present experimental results all cells are equivalent until compaction since they are not distinguished by the TC field in normal development. Interphase cells exhibit homogeneous mitochondrial activity, or perinuclear, or perinuclear and cortical activity, and these patterns too and the rotational symmetry observed are predicted by TC theory. The first differentiation, into an inner mass cell and the trophectoderm, as well as the formation of cell polarity in the trophectoderm are considered. It is suggested that these two events are driven by a peripheral spherical shell of high energy metabolism in the morula; such a shell is predicted by TC theory in a compacted multicellular sphere whose cells are connected by gap junctions. The experimental patterns of mitochondrial activity in unfertilized oocytes exhibit rotational symmetry or polarity. The shape and the chemical nature of these patterns also are predicted and explained by TC theory in a sphere. The change in the spatial pattern of mitochondrial activity with development is attributed to a change in the spatial pattern of mitochondrial activity and not to physical translocation of mitochondria. The experimental finding that these spatial patterns of mitochondrial activity are observed only in live and not in dead biological material is explained by the TC pattern being biology's unique and universal dissipative structure that requires ongoing specific biochemical reactions and energy dissipation.     

Isoelectric focusing--polynucleotide/polyacrylamide-gel electrophoresis. A technique to separate and characterize nuclease activities.

Individual native nuclease activities from human leucocytes are separated by using two-dimensional gel electrophoresis in an apparatus that allows the simultaneous running of 28 gels. Proteins are separated by isoelectric focusing in a disc gel, followed by electrophoresis into a slab gel containing DNA. Protein denaturants are avoided in the second dimension by the use of a running pH well above the optimal pH for DNAase (deoxyribonuclease) activity. Electrophoresed gels are incubated in appropriate buffers to activate nuclease activity. After staining for intact DNA, the positions of active enzymes, unobscured by the presence of other proteins, are revealed as colourless spots in a reddish-purple field. The technique is easy to use and is sensitive to 50pg of DNAase I. Versatility is provided by the use of either acidic or basic electrophoresis running buffers and by the use of specific gel incubation conditions to reveal different sets of enzyme activities. Two DNAases active at pH 7.4 in the presence of Mg2+ and Ca2+, and sixteen DNAases active at acidic pH and not requiring metals, are detected. Treatment of the human enzymes with specific glycosidases reveals that many of the human DNAases are glycoproteins containing negatively charged moieties and may be derived from modification of parent activities.     

Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with nuclear magnetic resonance

The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility, and amino acid composition of involved surface loops. As a model for such surface loops, we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by a covalent ring closure integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis state and an elongated trans state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics (MD) simulations. Prototypical conformations and the free-energy landscapes in the high-dimensional space spanned by the phi/psi angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open-loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open-loop conformations are missing in the refined NMR structures.     

Ultrastructure of the foregut and associated glands of Calicotyle kröyeri (Monogenea: Monopisthocotylea)

The mouth, pharynx and oesophagus of Calicotyle are lined by syncytial epithelia, and there are numerous unicellular glands associated with the oesophagus. An infolding of unmodified external tegument lines the mouth cavity and is connected by discrete cytoplasmic processes to subjacent perikarya. It contains two types of secretory body and its luminal surface is invested with a finely filamentous coating. The pharynx and oesophagus are lined by irregularly-folded epithelia that are interconnected by a septate desmosome. Membranous inclusions distinguish the pharynx epithelium and there is a well developed basal lamina for insertion of the pharyngeal muscles. The oesophagus epithelium is perforated by the openings of the oesophageal glands. These lie in the surrounding parenchyma and produce a dense, membrane-bound secretion which is conveyed by duct-like extensions of the glands to the oesophagus lumen. The ducts are supported in places by microtubules and are anchored to the oesophageal epithelium by septate desmosomes. A septate desmosome also marks the junction between the epithelium and the gut caeca.     

Study of the regulation of plastid development in Euglena gracilis. II. Functional localisation and synthesis of ribosomal chloroplast particles (author's transl)]

Chloroplast ribosomes in greening cells of Euglena gracilis are found either in the stroma or bound to thylakoid membranes. The membrane-bound chloroplast ribosomes are of two main types: those which can be released by 0.5 M KCl or by puromycin and 0.5 M KCl, and those which are released by detergent (deoxycholate or Triton X-100) and KCl. The ribosomes which are released by puromycin are presumably bound to chloroplast membrane by nascent peptide chains. Ribosomes released by puromycin are found only during the course of plastidial differentiation at the time of active thylacoid membrane synthesis. Following greening, those ribosomes remain bound to the membranes but can be removed by KCl alone. An analysis of RNA labelling showed that 30-S but not 53-S subunits of membrane-bound ribosomes are of uniform specific activity. This suggests that 30-S subunit exchange in a common pool while 53 S subunits remain membrane bound and do not exchange in a common pool. Membrane-bound chloroplast ribosomes which are released either by puromycin or by detergent are originally derived from loosely bound particles, released by 0.5 M KCl.     

The nature of stacking equilibria in polynucleotides

Temperature melting profiles of adenylyladenosine and cytidylylcytidine were examined by ultraviolet absorption, circular dichroism, and optical rotatory dispersion. They showed the following characteristics: profiles for different absorption wavelengths are identical as defined by least-squares computed optical and thermodynamic parameters; melting curves obtained by the three spectroscopic methods are likewise in all cases identical by a series of criteria; in terms of the operational equilibrium constant for base-stacking all van't Hoff plots are linear; absorption spectra and circular dichroism curves at a series of temperatures for both dinucleoside phosphates give excellent isosbestic points; a matrix-rank analysis of the family of complete spectra at different temperatures gives a value of two for the numbers of components in both cases. Four criteria are thus fulfilled of a two-state system for the stacking equilibrium. The results are not compatible with a multi-state scheme in which the substates are optically distinguishable. There is no measurable effect of ionic strength up to 1.0. In a presence of high concentrations of lithium chloride the criteria for two-state behavior are no longer fulfilled, and examination of infrared spectra gives evidence of complex formation by this salt, though not by sodium chloride. A destacking profile, similar to that observed on heating, is obtained by progressive addition of ethylene glycol to the solution. It is suggested that in dimers, though not in higher oligomers or polymers, the stacking equilibrium can be operationally regarded as a two-state system, and that the meaningful thermodynamic parameters can be extracted by analytical treatment, of the type here developed, of the melting profiles.     

Fine structure and functional role of the coverings of the eggs inMesostoma ehrenbergii (Focke) (Turbellaria,Neorhabdocoela)

Summary European populations of the turbellarianMesostoma ehrenbergii can produce two types of eggs according to a seasonal cycle. Subitaneous eggs (S eggs) are produced throughout the warm season and develop rapidly inside the parental uteri. They are meant to ensure a fast increase in the number of worms. Dormant eggs (D eggs) are produced during the warm season and are usually deposited in water at the death of the parent. They can hatch at the beginning of the next warm season and are, therefore, meant to ensure the survival of the population throughout the cold season, when adult worms are no longer present.S eggs are bounded by a thin, translucent covering which has a loose structure and is mainly proteinaceous in composition. These characteristics account for the functional role played by the S egg covering during embryonic development. The covering has, in fact, to be permeable to parental nutrients, and to keep pace, by stretching, with the enlargement of the embryo. By contrast, D eggs are bounded by a thick shell, presumably composed of a sclerotin, the precursors of which (polyphenols) are synthesized together with yolk in the vitelline cells. The shell has a smooth surface devoid of pores and has the function of isolating the developing D egg from the external environment.Supported by a grant from the Consiglio Nazionale della RicercheThe authors wish to thank Dr. P. Roach for his help in translating the paper     

Centrosomal and non-centrosomal microtubules.

While microtubule (MT) arrays in cells are often focused at the centrosome, a variety of cell types contain a substantial number of non-centrosomal MTs. Epithelial cells, neurons, and muscle cells all contain arrays of non-centrosomal MTs that are critical for these cells' specialized functions. There are several routes by which non-centrosomal MTs can arise, including release from the centrosome, cytoplasmic assembly, breakage or severing, and stabilization from non-centrosomal sites. Once formed, MTs that are not tethered to the centrosome must be organized, which can be accomplished by means of self-organization or by capture and nucleation of MTs where they are needed. The presence of free MTs requires stabilization of minus ends, either by MT-associated proteins or by an end-capping complex. Although some of the basic elements of free MT formation and organization are beginning to be understood, a great deal of work is still necessary before we have a complete picture of how non-centrosomal MT arrays are assembled in specific cell types.     

Biodiversity in agricultural landscapes: the ground beetle communities of woody uncultivated habitats

Agricultural landscapes can be defined as mosaics of landscape elements which are affected by farming practices. Woodland habitats, even though they are managed, are amongst the most stable elements of agricultural landscapes and can play a key role in the maintenance of biodiversity. This study of the ground beetle (carabid) communities of woodlands and woody linear features in a Scottish agricultural landscape shows that these habitats contribute significantly to the overall landscape diversity of these beetles. Communities in woods and hedgerows display the same species diversity and are both characterized by the presence of forest species. The main factors constraining carabid communities in both environments are the grazing intensity and, to a lesser extent, the type of soil. Heavily grazed locations are characterized by the occurrence of grassland species while forest species are restricted to ungrazed locations. At the landscape scale, the distribution of the forest species is limited by spatial isolation, indicating that there are insufficient functional links between woodland habitats in the study area. Isolation could be compensated for either by a better control of grazing so that linear features can be used as dispersal corridors for forest carabids or by planting more linear features and woods in the area.     

Replication and mutation on neutral networks

Folding of RNA sequences into secondary structures is viewed as a map that assigns a uniquely defined base pairing pattern to every sequence. The mapping is non-invertible since many sequences fold into the same minimum free energy (secondary) structure or shape. The pre-images of this map, called neutral networks, are uniquely associated with the shapes and vice versa. Random graph theory is used to construct networks in sequence space which are suitable models for neutral networks. The theory of molecular quasispecies has been applied to replication and mutation on single-peak fitness landscapes. This concept is extended by considering evolution on degenerate multi-peak landscapes which originate from neutral networks by assuming that one particular shape is fitter than all the others. On such a single-shape landscape the superior fitness value is assigned to all sequences belonging to the master shape. All other shapes are lumped together and their fitness values are averaged in a way that is reminiscent of mean field theory. Replication and mutation on neutral networks are modeled by phenomenological rate equations as well as by a stochastic birth-and-death model. In analogy to the error threshold in sequence space the phenotypic error threshold separates two scenarios: (i) a stationary (fittest) master shape surrounded by closely related shapes and (ii) populations drifting through shape space by a diffusion-like process. The error classes of the quasispecies model are replaced by distance classes between the master shape and the other structures. Analytical results are derived for single-shape landscapes, in particular, simple expressions are obtained for the mean fraction of master shapes in a population and for phenotypic error thresholds. The analytical results are complemented by data obtained from computer simulation of the underlying stochastic processes. The predictions of the phenomenological approach on the single-shape landscape are very well reproduced by replication and mutation kinetics of tRNA(phe). Simulation of the stochastic process at a resolution of individual distance classes yields data which are in excellent agreement with the results derived from the birth-and-death model.     

Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry

The purification of protein complexes can be accomplished by different types of affinity chromatography. In a typical immunoaffinity experiment, protein complexes are captured from a cell lysate by an immobilized antibody that recognizes an epitope on one of the known components of the complex. After extensive washing to remove unspecifically bound proteins, the complexes are eluted and analyzed by mass spectrometry (MS). Transient complexes, which are characterized by high dissociation constants, are typically lost by this approach. In the present study, we describe a novel method for identifying transient protein-protein interactions using in vivo cross-linking and MS-based protein identification. Live cells are treated with formaldehyde, which rapidly permeates the cell membrane and generates protein-protein cross-links. Proteins cross-linked to a Myc-tagged protein of interest are copurified by immunoaffinity chromatography and subjected to a procedure which dissociates the cross-linked complexes. After separation by SDS-PAGE, proteins are identified by tandem mass spectrometry. Application of this method enabled the identification of numerous proteins that copurified with a constitutively active form of M-Ras (M-Ras(Q71L)). Among these, we identified the RasGAP-related protein IQGAP1 to be a novel interaction partner of M-Ras(Q71L). This method is applicable to many proteins and will aid in the study of protein-protein interactions.     

Accuracy of alternative representations for integrated biochemical systems

The Michaelis-Menten formalism often provides appropriate representations of individual enzyme-catalyzed reactions in vitro but is not well suited for the mathematical analysis of complex biochemical networks. Mathematically tractable alternatives are the linear formalism and the power-law formalism. Within the power-law formalism there are alternative ways to represent biochemical processes, depending upon the degree to which fluxes and concentrations are aggregated. Two of the most relevant variants for dealing with biochemical pathways are treated in this paper. In one variant, aggregation leads to a rate law for each enzyme-catalyzed reaction, which is then represented by a power-law function. In the other, aggregation produces a composite rate law for either net rate of increase or net rate of decrease of each system constituent; the composite rate laws are then represented by a power-law function. The first variant is the mathematical basis for a method of biochemical analysis called metabolic control, the latter for biochemical systems theory. We compare the accuracy of the linear and of the two power-law representations for networks of biochemical reactions governed by Michaelis-Menten and Hill kinetics. Michaelis-Menten kinetics are always represented more accurately by power-law than by linear functions. Hill kinetics are in most cases best modeled by power-law functions, but in some cases linear functions are best. Aggregation into composite rate laws for net increase or net decrease of each system constituent almost always improves the accuracy of the power-law representation. The improvement in accuracy is one of several factors that contribute to the wide range of validity of this power-law representation. Other contributing factors that are discussed include the nonlinear character of the power-law formalism, homeostatic regulatory mechanisms in living systems, and simplification of rate laws by regulatory mechanisms in vivo.     

Two distinct classes of prestalk-enriched mRNA sequences in Dictyostelium discoideum

We have isolated cDNA clones derived from three mRNA sequences which are inducible by DIF, the putative stalk-specific morphogen of Dictyostelium. The three mRNA sequences are selectively expressed in cells on the stalk cell pathway of differentiation and we have compared them with previously characterized prestalk-enriched mRNA sequences. We find these latter sequences are expressed without a dependence on DIF, are much less highly enriched in prestalk over prespore cells and are expressed earlier during development than the DIF-inducible mRNA sequences. We propose two distinct mechanisms whereby a mRNA may become enriched in prestalk cells. An apparently small number of genes, represented by those we have isolated, is inducible by DIF and accumulates only in prestalk cells. We suggest that a second class of prestalk-enriched mRNA sequences are induced by cAMP to accumulate in all cells during aggregation and then become enriched in prestalk cells by selective loss from prespore cells.