Coding of visual objects in the ventral stream

How are objects represented in the brain? Two facets of this question are currently under investigation. First, are objects represented by activity in a relatively small number of neurons that are each selective for the shape or identity of a specific object (a 'sparse code'), or are they represented by a pattern of activity across a large number of less selective neurons (a 'population code')? Second, how are the neurons that code for an object distributed across the cortex: are they clustered together in patches, or are they scattered widely across the cortex? The results from neurophysiology and functional magnetic resonance imaging studies are beginning to provide preliminary answers to both questions.     

Allelic Negative Complementation at the Abruptex Locus of DROSOPHILA MELANOGASTER

The mutations of the Abruptex locus in Drosophila melanogaster fall into three categories. There are recessive lethal alleles and viable alleles. The latter can be divided into suppressors and nonsuppressors of Notch mutations. The recessive lethals are lethal in heterozygous combination with Notch. As a rule the recessive lethals are lethal also in heterozygous combination with the viable alleles. Heterozygous combinations of certain viable alleles are also lethal. In such heterozygotes, one heteroallele is a suppressor of Notch and the other is a nonsuppressor. Other heterozygous combinations of viable alleles are viable and have an Abruptex phenotype. The insertion of the wild allele of the Abruptex locus as an extra dose (carried by a duplication) into the chromosomal complement of the fly fully restores the viability of the otherwise lethal heterozygotes if two viable alleles are involved. The extra wild allele also restores the viability of heterozygotes in which a lethal and a suppressor allele are present. If, however, a lethal and a nonsuppressor are involved, the wild allele only partly restores the viability, and the effect of the wild allele is weakest if two lethal alleles are involved. It seems likely that of the viable alleles the suppressors of Notch are hypermorphic and the nonsuppressors are hypomorphic. The lethal alleles share properties of both types, and are possibly antimorphic mutations. It is suggested that the locus is responsible for a single function which, however, consists of two components. The hypermorphic mutations are defects of the one component and the hypomorphic mutations of the other. In heterozygotes their cumulative action leads to decreased viability. The lethal alleles are supposed to be defects of the function as a whole. The function controlled by the locus might be a regulative function.     

Graphs, random sums, and sojourn time distributions, with application to ion-channel modeling.

This paper considers the distribution of a sojourn time in a class of states of a stochastic process having finite discrete state space where sojourn times in any individual state are independent and identically distributed, and transitions between states follow a Markov chain. The state space and possible transitions of the process are represented by a graph. Class sojourn time distributions are derived by modifying this graph using 'composition' of states, defining a new Markov chain on the modified graph, and expressing the sojourn time in a composition state as a random sum. Appropriate compositions are chosen according to the possible "cores" of sojourns in the particular class, where a core describes the structure of a sojourn in terms of a single state or a chain in the original graph. Graph methods provide an algorithmic basis for the derivation, which can be simplified by using symmetry results. Models of ion-channel kinetics are used throughout for illustration; class sojourn time distributions are important in such models because individual states are often indistinguishable experimentally. Markov processes are the special case where sojourn times in individual states are exponentially distributed. In this case kinetic parameter estimation based on the observed class sojourn time distribution is briefly discussed; explicit estimating equations applicable to sequential models of nicotinic receptor kinetics are given.     

Modeling capsid self-assembly: design and analysis

A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible and an explicit solvent is optionally included. Model design, simulation methodology and analysis techniques are discussed. The analysis focuses on the growth pathways and the nature of the intermediate states, properties that are hard to access experimentally. Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered.     

Ultrastructure of muscle cells in Siboglinum fiordicum (Pogonophora)

Two different muscle types are found in the body of Siboglinum fiordicum: body wall muscle and blood vessel muscle. Both are of a myomesothelial type. The myofibrils of the body wall muscle are non-striated and consist of thick and thin myofilaments. Scattered dense bodies and attachment plaques are described. The sarcoplasmic reticulum forms a three-dimensional network in the myofibrils and only peripheral couplings are observed. The thick filaments are of a paramyosin type and have a diameter ranging from 400-1500 A. The blood vessels muscle is non-striated, but sometimes a sarcomere-like organization has been observed. Both thick and thin filaments are present. The thick filaments have a diameter of 250-400 A and lack transverse striations. Dense bodies and attachment of plaques are few. The sparse sarcoplasmic reticulum is restricted to the myofibril periphery where it makes peripheral couplings with sarcolemma. The luminal surface of the vessels is lined by a basal lamina with collagen-like inclusions. No endothelium is found. The body wall muscle and the blood vessel muscle are compared with other muscle types described in invertebrates.     

Similar and divergent features in mammalian and yeast prions

Mammalian transmissible spongiform encephalopathies are likely due to the propagation of an abnormal form of a constitutive protein instead of traditional genetic material (nucleic acids). Such infectious proteins, which are termed prions, exist in yeast. They are at the origin of a number of phenotypes that are inherited in a non-Mendelian manner. These prions are very useful to dissect the molecular events at the origin of this structure-based inheritance. The properties of mammalian and yeast prions are presented and compared. This review highlights a number of similarities and differences.     

Epidemiological models for heterogeneous populations: proportionate mixing,parameter estimation,and immunization programs

Deterministic models are presented for epidemics which occur quickly and for long-term endemic diseases where births and deaths must be considered. Contact-rate matrices are formulated in terms of activity levels and subpopulation sizes by using a proportionate-mixing assumption. Methods are presented for estimating epidemic and endemic parameters in both homogeneous and heterogeneous populations. Other authors' approaches to contact-rate matrices and spatial heterogeneity are described. Three immunization programs are analyzed for a model of a spatially heterogeneous population and are compared in a “city and villages” example.     

Nonlinear theory of ion-acoustic waves in an ideal plasma with degenerate electrons

A nonlinear theory is constructed that describes steady-state ion-acoustic waves in an ideal plasma in which the electron component is a degenerate Fermi gas and the ion component is a classical gas. The parameter ranges in which such a plasma can exist are determined, and dispersion relations for ion-acoustic waves are obtained that make it possible to find the linear ion-acoustic velocity. Analytic gas-dynamic models of ion sound are developed for a plasma with the ion component as a cold, an isothermal, or an adiabatic gas, and moreover, the solutions to the equations of all the models are brought to a quadrature form. Profiles of a subsonic periodic and a supersonic solitary wave are calculated, and the upper critical Mach numbers of a solitary wave are determined. For a plasma with cold ions, the critical Mach number is expressed by an explicit exact formula.     

A unified parametric regression model for recapture studies with random removals in continuous time

Conditional likelihood based on counting processes are combined with a Horvitz-Thompson estimator to yield a population size estimator that is more efficient than the existing ones. Random removals are allowed in the recapturing process. Simulation studies are shown to assess the performance of the proposed estimators. Examples on a bird banding and a small mammal recapturing study are given.     

THE MAINTENANCE OF GYNODIOECY AND ANDRODIOECY IN A METAPOPULATION

Males and females are at a selective disadvantage relative to hermaphrodites (cosexuals) in species with a colonizing habit, as only cosexuals are able to establish new colonies on their own. The implications of this disadvantage are assessed by means of a computer model of metapopulation dynamics, in which individual colonies are established through different rates of immigration and suffer different rates of local extinction. Results are given for simulations of an island model, a stepping-stone model, and for a partial analysis of the island model with simplifying assumptions. It is shown that: (1) unisexual frequencies in a metapopulation can be reasonably approximated by a linear function of the logarithm of the ratio of the immigration rate to the colony extinction rate; (2) metapopulation dynamics favor the maintenance of females (gynodioecy) over males (androdioecy) with cosexuals when they would otherwise be equally likely in a panmictic situation; (3) the way in which extinction and immigration rates affect unisexual frequencies at metapopulation equilibrium interacts with whether sterility is determined by a dominant or a recessive allele; and (4) unisexual frequencies are affected in a qualitatively similar way by the dynamics of a metapopulation when cosexuals are self-incompatible to when they are self-compatible, although only in the former case are high frequencies of unisexuals maintained when extinction and colonization rates approach the threshold at which the metapopulation goes extinct. These results are discussed with reference to existing data from species with nuclear male or female sterility.     

Two arms are better than one: parasite variation leads to combined inducible and constitutive innate immune responses

Parasites represent a major threat to all organisms which has led to the evolution of an array of complex and effective defence mechanisms. Common to both vertebrates and invertebrates are innate immune mechanisms that can be either constitutively expressed or induced on exposure to infection. In nature, we find that a combination of both induced and constitutive responses are employed by vertebrates, invertebrates and, to an extent, plants when they are exposed to a parasite. Here we use a simple within-host model motivated by the insect immune system, consisting of both constitutive and induced responses, to address the question of why both types of response are maintained so ubiquitously. Generally, induced responses are thought to be advantageous because they are only used when required but are too costly to maintain constantly, while constitutive responses are advantageous because they are always ready to act. However, using a simple cost function but with no a priori assumptions about relative costs, we show that variability in parasite growth rates selects for a strategy that combines both constitutive and induced defences. Differential costs are therefore not necessary to explain the adoption of both forms of defence. Clearly, hosts are likely to be challenged by variable parasites in nature and this is sufficient to explain why it is optimal to deploy both arms of the innate immune system.     

Rotary-shadowed freeze-fracture replicas: a simple method for the analysis of fracture faces

In rotary-shadowed freeze-fracture replicas, intramembrane particles on the periphery of a membrane fracture face are not uniformly shadowed from all sides. Those eccentrically positioned intramembrane particles with a net centripetally directed shadowing are on a convex fracture face. In contrast, those eccentrically positioned intramembrane particles with a net centrifugally directed shadowing are on a concave fracture face. Centrally positioned intramembrane particles on convex faces are uniformly shadowed from all sides; however, central depressions of concave faces are often unshadowed.     

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.     

How do potentials derived from structural databases relate to “true” potentials?

Knowledge-based potentials are used widely in protein folding and inverse folding algorithms. Two kinds of derivation methods are used. (1) The interactions in a database of known protein structures are assumed to obey a Boltzmann distribution. (2) The stability of the native folds relative to a manifold of misfolded structures is optimized. Here, a set of previously derived contact and secondary structure propensity potentials, taken as the "true" potentials, are employed to construct an artificial protein structural database from protein fragments. Then, new sets of potentials are derived to see how they are related to the true potentials. Using the Boltzmann distribution method, when the stability of the structures in the database lies within a certain range, both contact potentials and secondary structure propensities can be derived separately with remarkable accuracy. In general, the optimization method was found to be less accurate due to errors in the "excess energy" contribution. When the excess energy terms are kept as a constraint, the true potentials are recovered exactly.     

Enzyme deactivation

Enzyme deactivation kinetics is often first-order. Different examples of first-order deactivation kinetics exhibited by different enzymes under a wide variety of conditions are presented. Examples of both soluble and immobilized enzymes are presented. The influence of different parameters, chemical modification of specific residues, inhibitors, inactivators, protecting agents, induced conformational changes by external agents, enzyme concentration, and different substrates on the first-order inactivation kinetics of different enzymes is analyzed. The different examples presented from a variety of different areas provides a judicious framework and collection demonstrating the wide applicability of first-order deactivation kinetics. Examples of reversible first-order deactivation kinetics and deactivation-disguise kinetics are also presented.Different mechanisms are also presented to model complex enzyme deactivations. The non-series type mechanisms are emphasized and these involve the substrate and chemical modifiers. Substrate-dependent deactivation rate expressions that are of "separable" and "non-separable" type are presented. Rate expressions involving time-dependent rate constants along with their corresponding mechanisms are presented. Examples of enzymes that exhibit a deactivation-free grace period are also given. An interesting case of enzyme inactivation is the loss of activity in the presence of an auto-decaying reagent. The method is presented by which the intrinsic inactivation rate constants may be obtained. Examples of pH-dependent enzyme inactivation are presented that may be modelled by a five-step (or a simplified two-step) mechanism, and also by a single-step mechanism involving residual activity for the final state. Appropriate examples of enzyme inactivation are presented in each case to highlight the different mechanisms involved.     

Rotary-Shadowed Freeze-Fracture Replicas: A Simple Method for the Analysis of Fracture Faces

In rotary-shadowed freeze-fracture replicas, intramembrane particles on the periphery of a membrane fracture face are not uniformly shadowed from all sides. Those eccentrically positioned intramembrane particles with a net centripetally directed shadowing are on a convex fracture face. In contrast, those eccentrically positioned intramembrane particles with a net centrifugally directed shadowing are on a concave fracture face. Centrally positioned intramembrane particles on convex faces are uniformly shadowed from all sides; however, central depressions of concave faces are often unshadowed.     

Crustacean peptide and peptide-like pheromones and kairomones

Crustacean peptide pheromones, kairomones, and substituted amino sugar kairomones are reviewed from a historical perspective. These crustacean information molecules are secondary functions of structural polymers. They are partial hydrolysis products, generated usually by the action of trypsin-like enzymes on proteins, and glycosidase enzymes on glycoproteins and proteoglycans. Structure-function studies based upon synthetic mimics of peptide information molecules show neutral amino acids with a basic carboxyl terminal are active in modifying physiological and or behavioral responses. Behaviorally active substituted amino sugar mimics are disaccharide hydrolysis products of heparin and chondroitin sulfate. Similar molecules are also used as information molecules by a variety of other marine organisms indicating they are a common biological theme.     

Phylogeny and Biogeography of the Stapeliads

The stapeliads (Apocynaceae — Asclepiadoideae — Ceropegieae) form a group of highly succulent, practically leafless plants with a very diverse floral morphology. They are found in the drier parts of the Old World from southern Africa eastwards to Burma. 55 characters are selected on which a cladistic analysis is based and these are discussed in detail where necessary. From this a phylogeny is produced for the stapeliads. It is shown that they are monophyletic and that they are nested within a larger group among the tribe Ceropegieae of the subfamily Asclepiadoideae. Several of the important innovations that have led to the diversification of the stapeliads in semidesertic regions are discussed. The stapeliads appear to be mainly fly-pollinated. The methods of attraction of flies are mentioned and it is suggested that there are four basic floral types among the stapeliads.     

Regular and stochastic decays of waves in a plasma cavity

The regular and stochastic decays of fast high-frequency waves in a cavity filled with a low-density magnetoactive plasma are studied both theoretically and experimentally. The conditions for the transformation of the regular regime into the stochastic one are determined. The theoretical and experimental results are in a good agreement. Possible applications of stochastic decay are discussed.