Ewens' sampling formula and related formulae: combinatorial proofs, extensions to variable population size and applications to ages of alleles

Ewens' sampling formula, the probability distribution of a configuration of alleles in a sample of genes under the infinitely-many-alleles model of mutation, is proved by a direct combinatorial argument. The distribution is extended to a model where the population size may vary back in time. The distribution of age-ordered frequencies in the population is also derived in the model, extending the GEM distribution of age-ordered frequencies in a model with a constant-sized population. The genealogy of a rare allele is studied using a combinatorial approach. A connection is explored between the distribution of age-ordered frequencies and ladder indices and heights in a sequence of random variables. In a sample of n genes the connection is with ladder heights and indices in a sequence of draws from an urn containing balls labelled 1,2,...,n; and in the population the connection is with ladder heights and indices in a sequence of independent uniform random variables.     

Conditions for the Existence of Clines

A very general partial differential equation in space and time satisfied by the gene frequency in a monoecious population distributed continuously over an arbitrary habitat is derived. The treatment is restricted to a single diallelic locus in the absence of mutation and random drift, and it is supposed that time is continuous, births and deaths occur at random, and migration is independent of genotype. With the further assumptions that migration is isotropic and homogeneous, the population density is constant and uniform (as permitted by the population regulation mechanism included in the formulation), and Hardy-Weinberg proportions obtain locally, this partial differential equation reduces to the simplest multidimensional generalization of the classical Fisher-Haldane cline model. The efficacy of migration and selection in maintaining genetic variability at equilibrium in this model is investigated by deducing conditions for the existence of clines under various circumstances. The effects of the degree of dominance, a neutral belt between the regions where a particular allele is advantageous and deleterious, finiteness of the habitat, and habitat dimensionality are evaluated. Provided at least one of the alleles is favored only in a finite region, excluding the special case in which its total effective selective coefficient is zero, if conditions for supporting a cline are too unfavorable because migration is too strong, selection is too weak, or both, a cline cannot exist at all. Thus, unless there is overdominance, the population must be monomorphic. It is possible for a cline which can barely exist under the prevailing ecological circumstances to show a large amount of variation in gene frequency.     

Does Computation Reveal Machine Cognition?

This paper seeks to understand machine cognition. The nature of machine cognition has been shrouded in incomprehensibility. We have often encountered familiar arguments in cognitive science that human cognition is still faintly understood. This paper will argue that machine cognition is far less understood than even human cognition despite the fact that a lot about computer architecture and computational operations is known. Even if there have been putative claims about the transparency of the notion of machine computations, these claims do not hold out in unraveling machine cognition, let alone machine consciousness (if there is any such thing). The nature and form of machine cognition remains further confused also because of attempts to explain human cognition in terms of computation and to model/simulate (aspects of) human cognitive processing in machines. Given that these problems in characterizing machine cognition persist, a view of machine cognition that aims to avoid these problems is outlined. The argument that is advanced is that something becomes a computation in machines only when a human interprets it, which is a kind of semiotic causation. From this it follows that a computing machine is not engaged in a computation unless a human interprets what it is doing; instead, it is engaged in machine cognition, which is defined as a member or subset of the set of all possible mappings of inputs to outputs. The human interpretation, which is a semiotic process, gives meaning to what a machine does, and then what it does becomes a computation.     

江苏泗洪下草湾中中新世脊椎动物群——6.鸟纲

本文记述了近年来在江苏泗洪下草湾组中补采到的6种鸟类,其中包括天岗琵鹭 Platalea tiangangensis sp. nov.和松林庄古石鸡 Palaeoalectoris songlinensis gen. et sp. nov.,前者系琵鹭属迄今最早的记录,后者为雉科鹑族目前已知最早的成员.     

四种菊头蝠染色体组型分析

本文分析了皮氏菊头蝠(R. pearsoni chinensis),鲁氏菊头蝠(R.rouxi sinicus),角菊头蝠(R.cornutus pumilus)及中菊头蝠(R.affinis)的常规核型,现报道如下。     

Fluorescence polarization immunoassay: detection of antibody to Brucella abortus

Fluorescence polarization immunoassay (FPA) is a homogeneous immunoassay useful for rapid and accurate detection of antibody or antigen. The principle of the assay is that a fluorescent dye (attached to an antigen or an antibody fragment) can be excited by plane-polarized light at the appropriate wavelength. As a rule, a small molecule rotates faster when in solution than a larger molecule. The rotation rate may be assessed by measuring light intensity in the vertical and horizontal planes. Generally, the time it takes a molecule to rotate through a given angle is an indication of its size. When a small molecule that rotates rapidly is bound to a larger molecule, the rotation rate is decreased and this decrease is measured. Because it is a primary antigen-antibody interaction, the rate of reaction is very rapid and usually a result may be obtained in minutes. This technology was applied to the detection of antibody to Brucella abortus in serum and milk, providing for the first time a rapid primary binding assay that is cost effective for use in the field.     

Optimal seasonal timing of univoltine and bivoltine insects

This study examines the optimal seasonal timing of the life cycle for univoltine and bivoltine insects, assuming that resource availability has a peak in the middle of a year and is symmetric around it. Results show that if the growth rate increases in proporrion to the bodyweight, bivoltine life cannot be optimal. If the growth rate is a power function of the bodyweight with a power smaller than unity, a symmetric bivoltine solution can be the optimal provided that the resource availability has a plateau in the middle of the season. If the resource availability has a sharp peak, the optimal pattern is an asymmetric bivoltine solution in which the larval periods of two generations differ in length. The bivoltine life cycle is more likely to be superior to the univoltine one if: growth is fast, suitable growing season is long, biomass loss during nonlarval stages is small, and egg size is small.     

Rhesus monkey apolipoprotein(a). Sequence, evolution, and sites of synthesis

Human lipoprotein(a) is a low density lipoprotein-like lipoprotein whose concentration in plasma is correlated with atherosclerosis. The characteristic protein component of lipoprotein(a) is apolipoprotein(a) (apo(a)) which is disulfide-linked to apolipoprotein B-100. Sequencing of rhesus monkey apo(a) cDNA suggests that this protein, like human apo(a), is highly similar to plasminogen. Sequence data suggests that a plasminogen-like protease activity and kringle 1-, 2-, 3-, and 5-like domains are unnecessary for apo(a) function, but a highly repeated kringle four-like domain is important. Liver is the major site of apo(a) RNA synthesis; reduced amounts of message were also found in testes and brain. Co-expression with apoB-100 and plasminogen in rhesus tissues is not mandatory.     

Structure and evolution of metareticulate pollen

In a palynological study of the Amaranthaceae, a peculiar type of reticulate pollen was found that is characterized by the presence of a porate aperture in each of the meshes of the reticulum. Previously, this type of pollen has been described as “reticulate”;. However, closer investigations show that the reticulum in pollen of Amaranthaceae is composed of mesoporia and pores. Consequently, this kind of reticulum represents a fundamentally different type, and is not homologous to the well known examples of pollen grains with a true reticulum (e.g. in Bromeliaceae, Lamiaceae). Therefore, the term “metareticulate”; is proposed (i.e., pantoporate pollen with a reticulum‐like structure of mesoporia and pores). The new term allows to distinguish between metareticulate and truely reticulate pollen, what is important in phylogenetic studies. Metareticulate pollen occurs only within lineages characterized by pantoporate pollen, and is found to be derived from pantoporate pollen in a cladistic analysis. Apart from the Amaranthaceae, metareticulate pollen evolved parallel in Vivianiaceae and Zygophyllaceae. In Caryophyllaceae and Convolvulaceae only a trend towards a metareticulation is observed. Metareticulate pollen is suggested as representing the highest developmental level in successiformy, which is one of the major patterns in pollen evolution leading from tricolpate to pantoporate grains.     

Murine numb regulates granule cell maturation in the cerebellum

Notch is a key regulator of vertebrate neurogenesis and the cytoplasmic adaptor protein Numb is a modulator of the Notch signaling pathway. To address the role of murine Numb in development of the central nervous system, we used a conditional gene ablation approach. We show that Numb is involved in the maturation of cerebellar granule cells. Although the specification of neural cell fates in the cerebellum is not affected in the absence of Numb, the transition from a mitotic progenitor to a mature granule cell is aberrant and migration of postmitotic granule cells to the internal granule cell layer is delayed. In some animals, this results in a complete agenesis of granule cells and a strong ataxia. We confirmed these findings in vitro and found that Numb-deficient cerebellar progenitor cells show a marked delay in granule cell maturation. Our results suggest that Numb plays a role in the transition of a mitotic progenitor to a fully differentiated granule cell in the cerebellum. In addition, the maturation of Purkinje cells is also delayed in Numb-deficient mice.     

Galectin-3 as a multifunctional protein

Galectin-3 is a 31 kDa member of a growing family of beta-galactoside-binding animal lectins. This protein is expressed in a variety of tissues and cell types and is mainly found in the cytoplasm, although, depending on cell type and proliferative state, a significant amount of this lectin can also be detected in the nucleus, on the cell surface or in the extracellular environment. Galectin-3 is secreted from cells by a novel and incompletely understood mechanism that is independent of the classical secretory pathway through the endoplasmic reticulum/Golgi network. Galectin-3 exhibits pleiotropic biological function, playing a key role in many physiological and pathological processes.     

Insights into rheumatoid arthritis derived from the Sa immune system

The Sa system is a recently described immune system that has a specificity and positive predictive value of nearly 100% for rheumatoid arthritis (RA) in Asia, Europe and the Americas. Its sensitivity of 30-40% suggests that it identifies a subset of RA patients. Anti-Sa antibodies are present from disease onset and are predictive of disease severity. The immune reactants are plentiful in the target tissue: antigen is present in the synovium, IgG antibody in the fluid. Immunologically, Sa is a hapten-carrier antigen in which vimentin is the carrier and citrulline is the hapten. The citrullination of vimentin is closely related to apoptosis, and citrullinated vimentin is extremely sensitive to digestion by the ubiquitous calpains. Nevertheless, Sa is found in only a few cell lines. Calpastatin, the natural specific inhibitor of calpains, is also a RA-associated, albeit non-specific, autoimmune system. Is it possible that calpain-related apoptotic pathways could be prominent in cells containing Sa? The task is to reconcile the specificity of Sa/citrullinated proteins in a multifactorial and polygenic disease such as RA.     

N-acetylaspartate in the vertebrate brain: metabolism and function

N-Acetyl-l-aspartate (NAA) is an amino acid that is present in the vertebrate brain. Its concentration is one of the highest of all free amino acids and, although NAA is synthesized and stored primarily in neurons, it cannot be hydrolyzed in these cells. Furthermore, neuronal NAA is dynamic and turns over more than once each day by virtue of its continuous efflux, in a regulated intercompartmental cycling via extracellular fluids, between neurons and a second compartment in oligodendrocytes. The metabolism of NAA, between its anabolic compartment in neurons and its catabolic compartment in oligodendrocytes, and its possible physiological role in the brain has been the subject of much speculation. There are two human inborn errors in metabolism of NAA. One is Canavan disease (CD), in which there is a buildup of NAA (hyperacetylaspartia) and associated spongiform leukodystrophy, caused by a lack of aspartoacylase activity. The other is a singular human case of lack of NAA (hypoacetylaspartia), where the enzyme that synthesizes NAA is apparently absent. There are two animal models currently available for studies of CD. One is a rat with a natural deletion of the catabolic enzyme, and the other a gene knockout mouse. In addition to the presence of NAA in neurons, its prominence in ¹H nuclear magnetic resonance spectroscopic studies has led to its wide use in diagnostic human medicine as both an indicator of brain pathology and of disease progression in a variety of CNS diseases. In this review, various hypotheses regarding the metabolism of NAA and its possible role in the CNS are evaluated. Based on this analysis, it is concluded that although NAA may have several functions in the CNS, an important role of the NAA intercompartmental system is osmoregulatory, and in this role it may be the primary mechanism for the removal of intracellular water, against a water gradient, from myelinated neurons.     

A bio-physical basis of mathematics in synaptic function of the nervous system: A theory

The purpose of this paper is to present a bio-physical basis of mathematics. The essence of the theory is that function in the nervous system is mathematical. The mathematics arises as a result of the interaction of energy (a wave with a precise curvature in space and time) and matter (a molecular or ionic structure with a precise form in space and time). In this interaction, both energy and matter play an active role. That is, the interaction results in a change in form of both energy and matter. There are at least six mathematical operations in a simple synaptic region. It is believed the form of both energy and matter are specific, and their interaction is specific, that is, function in most of the nervous system is stereotyped. It is suggested that mathematics be taken out of the mind and placed where it belongs — in nature and the synaptic regions of the nervous system; it results in both places from a precise interaction between energy (in a precise form) and matter (in a precise structure).Departments of Medicine, Presbyterian-University of Pennsylvania Medical Center and the University of Pennsylvania School of Medicine     

The lizard ear: Cordylus, Platysaurus and Gerrhosaurus

In further consideration of the lizard ear, the fine structure of the cochlea has been investigated and related to auditory sensitivity in members of the family Cordylidae. The ear of this group of lizards is unusual in that a tectorial membrane is present only in a modified and seemingly vestigial form, and this membrane makes no connections with the auditory hair cells. These cells are provided instead with a series of sallets, small bodies extending in a single row through the dorsal and middle regions of the cochlea, where they rest upon the tips of the ciliary tufts and evidently bring about a stimulation of the hair cells because of their inertia. At the ventral end of the cochlea this line of sallets ends, and here is a single, relatively enormous structure, the culmen papillae, that serves a similar purpose for a large group of hair cells. Consideration is given to the manner of stimulation of the auditory sense cells in these species in relation to others with the usual arrangements involving connections between the ciliary tufts and a tectorial membrane. Included also is a study of a species of Gerrhosaurus, which some have included in the cordylid family and others have placed in a family of its own. The cochlear structure in this species is similar to that of the cordylids in many respects but differs in the ventral region, where instead of the culmen there is a heavy tectorial plate, similarly covering a large number of hair cells but connected to a tectorial membrane. The functioning of these ears is assessed in terms of the cochlear potentials, and is found to vary with species from better than average to excellent in comparison with other lizards investigated. The structural differentiation also is of fairly high degree, and hence it appears that ears without tectorial connections, or with such connections only in a limited region of the cochlea, can perform in a highly serviceable manner.     

p53 chromatin epigenetic domain organization and p53 transcription

Epigenetic organization represents an important regulation mechanism of gene expression. In this work, we show that the mouse p53 gene is organized into two epigenetic domains. The first domain is fully unmethylated, associated with histone modifications in active genes, and organized in a nucleosome-free conformation that is deficient in H2a/H2b, whereas the second domain is fully methylated, associated with deacetylated histones, and organized in a nucleosomal structure. In mitotic cells, RNA polymerase is depleted in domain II, which is folded into a higher-order structure and is associated with H1 histone, whereas domain I conformation is preserved. Similar results were obtained for cells treated with inhibitors of associated regulatory factors. These results suggest that depletion of RNA polymerase II is the result of a physical barrier due to the folding of chromatin in domain II. The novel chromatin structure in the first domain during mitosis also suggests a mechanism for marking active genes in successive cell cycles.     

The mode of action of pyrethnxm on the cockroach, Periplaneta americana L

Pyrethrin, the active principle of pyrethrum powder, is insoluble in water but is soluble in, the body fluid of the cockroach. It has a selective action on nerve ganglia, and the destruction of their cells is responsible for the death of the insect. Whereas pyrethrum, when used -either in the powdered form or in a fluid state mixed with kerosene and introduced directly into the body cavity reaches the ganglion with the circulation, its mode of action when it acts through the spiracles is different. Kerosene-pyrethrum mixture when introduced into the tracheal trunks through the spiracles is quickly diffused into the haemocoele. When the dry powder is inserted into the trachea, its mode of action is analogous to a fluid preparation. As the conversion of pyrethrum from a dry into a fluid state is alone possible in the interior of the trachea, the natural conclusion is that a fluid analogous to the body fluid is present in the same situation. As soon as the pyrethrin is dissolved, it is quickly diffused into the haemocoele and thus reaches the nearest ganglion.