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.     

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.     

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.     

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.     

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.     

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.     

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.     

A search for conceptual congruence between individuals and species

A new argument that species are individuals has recently been presented based on the way species names are used and systemic logic. The alternate idea that species are a categorical item, i.e., collections of individuals, was rejected. We wanted to evaluate this approach by establishing concepts that apply to individuals in order to examine if they are also applicable to a species viewed as a categorical item. It is our thinking that if species are not such, then concepts applicable to individuals will not be applicable to species so viewed. Individuals and species are similar in the presence of conceptual boundaries, unidirectional change and the presence of past and future time. These are all central, and salient, biological phenomena. But, these are concepts that apply also to populations which, for the most part, are not the same as species. Thus, these considerations infer that species, when viewed as a collection of individuals, do not share relevant concepts with individuals. Our conclusion is that a species is a 'unity' rather than an 'individual'.     

高迁移率族蛋白成员HMG20a/b的研究进展

高迁移率族(HMG)蛋白是一类广泛存在的非组蛋白型染色体蛋白,能通过诱导染色质结构的变化影响DNA表达。HMG20a和HMG20b是一对高度同源的HMG家族蛋白,均含有一个结构保守的HMG-box结构域和一个coiled-coil结构域,在生物体内广泛表达。HMG20a/b在细胞核内参与组蛋白去甲基酶复合物LSD1-Co REST的形成及一系列与细胞分裂分化相关的生理进程,如神经细胞核红细胞的分化、细胞质分裂以及EMT过程。研究发现,HMG20a/b一些功能的发挥是通过LSD1-Co REST复合物来实现的;在神经分化过程中,HMG20a、HMG20b具有相互拮抗的作用;而HMG20a促进EMT过程反映它很可能是一个促癌因子。本文对HMG20a/b的结构和体内分布及生物学功能进行综述。     

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.     

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.     

Cladistic Analysis of A Problematic Ammonite Group: the Hamitidae (Cretaceous, Albian–turonian) and Proposals for New Cladistic Terms

The Hamitidae are a family of mid–Cretaceous heteromorph ammonites including lineages leading to four other families. Problems are outlined in trying to describe the phylogeny of completely extinct groups such as these heteromorph ammonites using the existing cladistic terminology, which is largely concerned with extant taxa and their ancestors. To solve these problems, two new terms are proposed: †crown groups and †stem groups, which are equivalent to crown and stem groups in terms of the evolutionary history of a clade, but are not defined on the basis of extant taxa. Instead they are defined by the topology of the phylogenetic tree, the †crown group being a clade defined by synapomorphies but which gave rise to no descendants. A †stem group is a branch of a phylogenetic tree which comprises the immediate sister groups of a given †crown group but is not itself a clade. Examples of these terms are described here with reference to the phylogeny of the Hamitidae and their descendants. The Hamitidae are paraphyletic and form †stem groups to a number of †crown groups, namely the Anisoceratidae, Baculitidae, Scaphitidae, and Turrilitidae. The definitions of the genera and subgenera are refined with respect to the type species and the clades within which they occur, and four new genera are described: Eohamites , Helicohamites , Sziveshamites , and Planohamites .     

Vegetative anatomy of subtribe Orchidinae (Orchidaceae)

Leaves in Orchidinae are essentially glabrous; anticlinal walls of foliar epidermal cells arc basically straight-sided to curvilinear, and cells arc fundamentally polygonal on both surfaces; adaxial cells are larger than abaxial cells. Stomata arc anomocytic and usually only abaxial and superficial; substomatal chambers are small to moderate; outer and inner guard cell ledges are mostly small. There is no hypodermis nor are there fibre bundles. Mesophyll is homogeneous, chlorcnchyma cells arc thin-walled, and intercellular spaces numerous. Crystalliferous idioblasts abound. Vascular bundles are collateral, organized in a single series. and lack associated sclerenchyma. Bundle sheath cells are thin-walled and chlorophyllous. Stems are glabrous; stomata arc frequent in one species, lacking in others. Cortical cells are oval to circular, thick-walled, and interspersed with triangular intercellular spaces. Ground-tissue cells are circular, and triangular intercellular spaces are present. Vascular bundles arc collateral and scattered throughout the ground-tissue or are absent from the central ground-tissue. Epidermis in absorbing roots is one-layered and non-velamcntous. Exodcrmal cells are thin-walled and dead cell walls bear tenuous scalariform bars; some species lack an exodermis. Outer cortical cells are polygonal and lack intercellular spaces; middle layer cortical cells are rounded with triangular intercellular spaces; inner layer cells are polygonal and lack intercellular spaces. Endodermis and pericycle are thin-walled and one-layered. Vascular cylinder is mostly 7–9-arch with xylcm and phloem components alternating regularly; vascular tissue is embedded in parenchyma; pith cells are parenchymatous, polygonal, thin-walled and lack intercellular spaces. Root tubers generally bear a velamen of variable thickness; bulbous-based unicellular hairs frequently form a dense mat; exodermal cells are thin-walled; dead cells have scalariform bars, passage cells are sparse. Ground-tissue consists of rounded water-storage and assimilatory cells interspersed with triangular or quadrangular intercellular spaces; peripheral cells arc polygonal lacking intercellular spaces. Vascular tissue consists of monarch to pentarch meristeles distributed thoughout the ground-tissue each surrounded by a uniscriale endodermis of thin-walled cells. Thin roots ofPlalanthera exhibit a typical central cylinder surrounded by a homogeneous cortex uninterrupted by meristeles; thicker roots show a central vascular cylinder and cortex in which meristeles are also present; in globoid root tubers there is no central cylinder, and the ground-tissue is replete with scattered meristeles. Because the central vascular cylinder in Platanthera gives rise to branches (meristeles), these represent components of a single vascular system and are not separate stelar entities as implied by the use of the term ‘polystele’.     

北京地区蕨类植物区系分析

对北京地区蕨类植物区系进行了初步分析,研究表明,北京共有蕨类植物77种,隶属于19科34属,以蹄盖蕨科、岩蕨科、鳞毛蕨科、卷柏科等为优势科,以岩蕨属、卷柏属、铁角蕨属等为优势属,科内及属内分化程度较低,种类组成贫乏;地理成分以温带成分占优势,有11属为温带分布属,占非世界分布属总数的61．11％,除世界种和中国特有种外,全为温带性质的种;生境特点以石生为主,大多数种类分布在北京西部和北部的山区;与河北的关系最为密切,其次为山西、内蒙、辽宁、山东,与秦岭也有一定的联系,与西藏的关系疏远。     

Evaluating “Hot Spots” of Soil Contamination (Redux)

Every day, thousands of soil samples are collected from properties suspected of being contaminated. The samples are sent to laboratories where the chemical constituents are quantified. Frequently, one or more samples are identified as constituting a “hot spot” of soil contamination. The consequences of such a determination—more sampling, more remediation, more reporting—are often quite expensive. Yet despite the often costly consequences of identifying a “hot spot,” there appears no supportable methodology for objectively deciding which spots are “hot” and which are “not.” This can lead to situations where sampling episodes are required to demonstrate that there is not a problem, even though just exactly what would comprise a “problem” is not particularly clear and sometimes is not stated. The authors provide a review and analysis of common and published information concerning “hot spots.” They then present a different point of view about “hot spots” from those in common practice, a point of view that will challenge many environmental professionals to reconsider how they evaluate sampling results.     

Italian palaeolithic and mesolithic burials

More than 50 skeletons have been found in Italy in Upper Palaeolithic and Mesolithic burials, most of them being of Pleistocene age. As for as Upper Palaeolithic is concerned, two distinct phases are recognized, with a gap in records between them of several millennia: 1) a first phase, in which rich burials, generally of adult or adolescent males, are found. Associated industries are of Gravettian — Early Epigravettian type. Strict rules are followed in funerary practices. Sites of this period are only a few in Italy, but most of them yelded burials; 2) a second phase, of late Würm IV age, with burials found in several sites all over Italy, associated with Final Epigravettian industries. Women as well as children are now buried in single graves, but men still outnumber women. Grave goods are scarce or lacking, except at Arene Candide, where very rich burials, customarily attributed to Mesolithic, but actually of Dryas III age, were found. Truly Mesolithic sepultures are only a few, and burial goods are scarce or lacking.     

Stochastic simulation of chemical reactions with spatial resolution and single molecule detail

Methods are presented for simulating chemical reaction networks with a spatial resolution that is accurate to nearly the size scale of individual molecules. Using an intuitive picture of chemical reaction systems, each molecule is treated as a point-like particle that diffuses freely in three-dimensional space. When a pair of reactive molecules collide, such as an enzyme and its substrate, a reaction occurs and the simulated reactants are replaced by products. Achieving accurate bimolecular reaction kinetics is surprisingly difficult, requiring a careful consideration of reaction processes that are often overlooked. This includes whether the rate of a reaction is at steady-state and the probability that multiple reaction products collide with each other to yield a back reaction. Inputs to the simulation are experimental reaction rates, diffusion coefficients and the simulation time step. From these are calculated the simulation parameters, including the 'binding radius' and the 'unbinding radius', where the former defines the separation for a molecular collision and the latter is the initial separation between a pair of reaction products. Analytic solutions are presented for some simulation parameters while others are calculated using look-up tables. Capabilities of these methods are demonstrated with simulations of a simple bimolecular reaction and the Lotka-Volterra system.