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.     

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.     

Mutants of Escherichia Coli with Increased Fidelity of DNA Replication

SINEs are short interspersed repeated DNA elements which are considered to spread throughout genomes via RNA intermediates. Polymorphisms with regard to the presence or absence of SINE are occasionally observed in a specific location of a genome. We modeled the evolution of SINEs with regard to this type of polymorphism. Because SINEs are rarely deleted, multiplication of elements is confined to a certain period, and a few master copies are considered to be responsible for their multiplication, the usual population genetic models of transposable elements assuming the equilibrium state are not applicable to describe the evolution of SINEs. Taking into account these properties and assuming selective neutrality, we computed conditional probabilities of finding a SINE at a specific site given that this site is first found because it is occupied by a SINE in an original sample. Using these probabilities, we investigated ways to estimate the multiplication period and infer relationships among populations. The latter inference procedures are shown to be strongly dependent on the multiplication period.     

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'.     

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.     

Thecal designs in isorophinid edrioasteroids

A study of functional morphology in the edrioasteroid suborder Isorophina reveals three major thecal designs: domal, pyrgate, and clavate. Pyrgate forms are characterized by specialized morphologic features that facilitate extension of the theca well above the substrate and contraction of the theca to a low, streamlined, domal profile. Domal forms have a low, domal thecal profile capable of little shape change. Clavate forms are characterized by modifications to the pyrgate theca to facilitate higher-level suspension feeding. Pyrgate species are generalized edrioasteroids that inhabited a variety of nearshore open-marine environments. Domal species are small specialized edrioasteroids that inhabited shallow-marine to intertidal environments. Clavate species inhabited offshore, open-marine environments. The size reduction of the peripheral rim and the modifications to the pedunculate zone are adaptations allowing clavate edrioasteroids to compete for small attachment sites while maintaining the ability to extend the theca for higher-level suspension feeding and respiration. A phylogenetic analysis of well-known isorophinid edrioasteroids to determine the relationships between the three designs indicates that domal species are a monophyletic group within the Isorophinidae, clavate species are a monophyletic group within the Agelacrinitidae, and isorophinid pyrgate species are a paraphyletic group ancestral to both domal and clavate forms. □ Edrioasteroidea, Echinodermata, functional morphology, phylogeny.     

A point process driven multiple change point model: A robust resistant approach

Helicases are a class of enzymes involved in Ribonucleic Acid (RNA) metabolism. In this work a statistical method is proposed to analyze the individual mechanistic cycle of these motor proteins which are crucial to the understanding of their cellular functions. The RNA unwinding by NS3 helicase is hypothesized to occur in a series of discrete steps and the steps themselves occurring in accordance to an underlying point process. A point process driven multiple change point model is proposed to model the RNA unwinding mechanism. The methods are portable to other areas of applications as well. Algorithms based on robust-resistant statistical procedures are proposed to detect the change points. Both sequential and a posteriori change point models are considered. The relevant parameters of interest are estimated using a maximum likelihood approach. Simulations are performed to assess the performance of the methodology.     

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.     

Adaptive change in the resource-exploitation traits of a generalist consumer: the evolution and coexistence of generalists and specialists

Mathematical models of consumer-resource systems are used to explore the evolution of traits related to resource acquisition in a generalist consumer species that is capable of exploiting two resources. The analysis focuses on whether evolution of traits determining the capture rates of two resources by a consumer species produce one generalist, two specialists, or all three types, when all types are characterized by a common fitness function. In systems with a stable equilibrium, evolution produces one generalist or two specialists, depending on the second derivative of the trade-off relationship. When there are sustained population fluctuations, the nature of the trade-off between the consumer's capture rates of the two resources still plays a key role in determining the evolutionary outcome. If the trade-off is described by a choice variable between zero and one that is raised to a power n, polymorphic states are possible when n > 1, which implies a positive second derivative of the curve. These states are either dimorphism, with two relatively specialized consumer types, or trimorphism, with a single generalist type and two specialists. Both endogenously driven consumer-resource cycles, and fluctuations driven by an environmental variable affecting resource growth are considered. Trimorphic evolutionary outcomes are relatively common in the case of endogenous cycles. In contrast to a previous study, these trimorphisms can often evolve even when new lineages are constrained to have phenotypes very similar to existing lineages. Exogenous cycles driven by environmental variation in resource growth rates appear to be much less likely to produce a mixture of generalists and specialists than are endogenous consumer-resource cycles.     

Characterization of scientific studies usually cited as evidence of adverse effects of GM food/feed

GM crops are the most studied crops in history. Approximately 5% of the safety studies on them show adverse effects that are a cause for concern and tend to be featured in media reports. Although these reports are based on just a handful of GM events, they are used to cast doubt on all GM crops. Furthermore, they tend to come from just a few laboratories and are published in less important journals. Importantly, a close examination of these reports invariably shows methodological flaws that invalidate any conclusions of adverse effects. Twenty years after commercial cultivation of GM crops began, a bona fide report of an adverse health effect due to a commercialized modification in a crop has yet to be reported.     

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 .     

The cercal receptor system of the praying mantid,Archimantis brunneriana Sauss.

Summary The cerci of the praying mantid, Archimantis brunneriana Sauss., are paired segmented sensory organs located at the tip of the abdomen. Basally the cercal segments are slightly flattened dorso-ventrally and are fused to such a degree that it is difficult to distinguish them. Distally the segments become progressively more flattened laterally and their boundaries become more obvious.Two types of sensilla are present on the cerci, trichoid sensilla and filiform sensilla. Trichoid hairs are longest on the medial side of the cerci and toward the cercal base. On the proximal cercal segments they are grouped toward the middle of each segment while they are more uniformly distributed on the distal segments. Filiform sensilla are found at the distal end of each segment except the last and are most abundant on the middle segments of the cercus. Both the number of cercal segments and the number of sensilla are variable. Trichoid hairs are highly variable in appearance from short and stout to long and thin. They arise from a raised base, have a fluted shaft, and some have a pore at the tip. They are innervated by from one to five dendrites, one of which is always considerably larger than the others. Some of the dendrites continue out into the shaft of the hair.Filiform hairs have fluted shafts and are mounted in a flexible membrane within a cuticular ring in a depression. They are innervated by a single large sensory neuron, the dendrite of which passes across a flattened area on the inner wall of the lumen of the hair. The dendritic sheath forms the lining of the ecdysial canal and is therefore firmly attached to the hair. The dendrite is attached to the sheath by desmosomes distally and is penetrated by projections of the sheath more proximally. A fibrous cap surrounds the dendrite and may hold it in place relative to the hair.The cercal receptor system of Archimantis is compared to those of cockroaches and crickets.     

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.     

Conflict and cooperation among the Vikings: Contingent behavioral decisions

We analyze historical accounts of Viking populations in Scotland and Iceland to show that considerations of kinship play a role in individuals' decisions on whether to engage in and revenge murder, as well as in the formation of alliances. However, willingness to murder a relative or to demand vengeance for the murder of another individual depends on the costs and benefits that accrue from the action, as well as the degree of relatedness. When the potential gains from murder are high, individuals are more willing to murder relatives; when the costs of exacting vengeance for a murder are high, individuals are more likely to settle for blood-money compensation for the murder of a family member. Alliances are more likely to be formed with relatives than between unrelated families; moreover, alliances with related individuals are less likely to involve preconditions and are more likely to be stable in the long term.     

Paraffin Embedding; a Graded-Temperature Table Used with Multiple Blocking for Enhanced Efficiency

Details are given for the construction of a graded-temperature table having a cool and hot side. Aluminum baking pans smeared with glycerol are used to cast the multiple paraffin blocks. These are loaded with paraffin wax from an electrically heated paraffin wax dispenser incorporated in the graded-temperature table and the pieces of tissue and labels orientated in them. The pans are then moved to the cool side of the table before finally floating them on cold water to harden the wax. Arranged above the heated side of the table are two infrared lamps which prevent premature solidification of the surface of the wax. After removing the solid, multiple-block slabs from the pans, the infrared lamps are used to soften the wax to a cheese-like consistency. Individual blocks are cut apart and trimmed around their sides with single strokes to produce smooth-sided blocks which are ready for attaching to wooden holders, adapted to the microtome chuck.     

Lipid-cholesterol interactions. Monte Carlo simulations and theory.

Results of Monte Carlo calculations of order parameter profiles of lipid chains interacting with cholesterol are presented. Cholesterol concentrations in the simulations are sufficiently large that it is possible to analyze profiles for chains which are near neighbors of two or more cholesterol molecules, chains which are neighbors to a single cholesterol, and chains which are not near any cholesterol molecules. The profiles, show that cholesterol acts to significantly decrease the ability of neighboring chains to undergo trans-gauche isomeric rotations, although these chains are not all forced into all-trans conformations. The effect is significantly greater for chains which are neighbors to more than one cholesterol. The Monte Carlo results are next used as a guide to develop a theoretical model for lipid-cholesterol mixtures. The properties of this model and the phase diagram which it predicts are described. The phase diagram is then compared with experimentally determined phase diagrams. The model calculations and the computer simulations upon which they are based yield a molecular mechanism for several of the observed phases exhibited by lipid-cholesterol mixtures. The theoretical model predicts that at low temperatures the system should exhibit solid phase immiscibility.     

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.     

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。     

Fixed and unstable I-related transposable elements in heterochromatin of Drosophila melanogaster

Transposable elements are disproportionately abundant in the heterochromatin of Drosophila melanogaster. Among the forces contributing to this bias in genomic distribution, fixation due to positive selection has been put forward. We have studied I-related elements which are located in pericentromeric heterochromatin and are believed to have a role in the control of active I elements. Flies straight from the wild have been studied where fixed elements are expected to emerge clearly over the highly polymorphic background in the genomic distribution of transposable elements. The results show that some restriction fragments due to I-related elements are conserved in size and are present in all individuals tested, consistent with a selective pressure for a role. Other fragments are polymorphic in presence/absence and intensity in individuals from the wild but appear homogeneous in laboratory stocks. Although the significance of this type of instability is unclear, the finding that these polymorphic bands are recurrent in populations from distant geographical locations is also suggestive of a selective pressure for a role.     

Leaf processing in a woodland stream*

Detritus processing by a small woodland stream is analysed by following the loss of weight of 10 g, single species accumulations of riparian leaves. The daily loss rates are expressed as exponential coefficients after the data are fitted by least squares. Comparisons are made between two sites on a small hardwater trout stream during two seasons. Leaf processing rates form a continuum from a low of 0.5%/day to a high of 2.0%/day. Differences between species of leaf are observed, but significant differences between fall and winter processing and between the two sites are not. The response of the invertebrate community to differences in leaf species is investigated using controlled, artificial streams where significant differences in the effect of the invertebrates are related to the ability ofthe leaf to be processed. Evidence suggests that differential invertebrate colonization of leaf packs is a function of microbial colonization and conditioning. The data are used to develop a general scheme of leaf pack processing.