World Models in Authors' Stories

The study of world models is currently in a growth phase as efforts are made to create theoretical frameworks and to refine instruments. At the same time, the empirical body of research is being expanded as more and more objects through which world models emerge are identified. Stories are one such object. It is generally known that this specific product of human culture provides very valuable material both for the analysis of psychological problems at the level of the individual and for the study of the attitudes and motivational determinants of society as a whole. In the modern world, stories function primarily as a special form of representation of existing models of reality and of their transmission to the younger generation. However, there appears to be a certain fundamental difference between author-written stories and folk tales, one having to do with the particular aspect of reality that is modeled in them. Folk tales (including folk tales "retold" by well-known compilers) are characterized by the presentation of the hero as an actor or agent and of the overall situation as one in which some goal is achieved. Authors' stories, on the other hand, as works of fiction, orient the reader mainly in the world of human relationships. Intentionally or not, they incorporate models of relationships that circulate in modern-day society. This allows them to be used as an object of study in the investigation of models of interpersonal relationships.     

Stage-specificity of spontaneous mutation at a tandem repeat DNA locus in the mouse germline

Mouse expanded simple tandem repeat (ESTR) loci are the most unstable loci in the mouse genome. Despite the fact that over the last decade these loci have been extensively used for studying germline mutation induction in mice, to date little is known about the mechanisms underlying spontaneous and induced ESTR mutation. Here we used flow cytometry and single-molecule PCR to compare the frequency of ESTR mutation in four flow-sorted fractions of the mouse male germ cells – spermatogonia, spermatocytes I, round and elongated spermatids. The frequency and the spectrum of ESTR mutation did not significantly differ between different stages of mouse spermatogenesis. Considering these data and the results of other publications, we propose that spontaneous ESTR mutation is mostly attributed to replication slippage in spermatogonia and these loci may be regarded as a class of expanded microsatellites.     

Ubiquitous expression of CUG or CAG trinucleotide repeat RNA causes common morphological defects in a Drosophila model of RNA-mediated pathology

Expanded DNA repeat sequences are known to cause over 20 diseases, including Huntington's disease, several types of spinocerebellar ataxia and myotonic dystrophy type 1 and 2. A shared genetic basis, and overlapping clinical features for some of these diseases, indicate that common pathways may contribute to pathology. Multiple mechanisms, mediated by both expanded homopolymeric proteins and expanded repeat RNA, have been identified by the use of model systems, that may account for shared pathology. The use of such animal models enables identification of distinct pathways and their 'molecular hallmarks' that can be used to determine the contribution of each pathway in human pathology. Here we characterise a tergite disruption phenotype in adult flies, caused by ubiquitous expression of either untranslated CUG or CAG expanded repeat RNA. Using the tergite phenotype as a quantitative trait we define a new genetic system in which to examine 'hairpin' repeat RNA-mediated cellular perturbation. Further experiments use this system to examine whether pathways involving Muscleblind sequestration or Dicer processing, which have been shown to mediate repeat RNA-mediated pathology in other model systems, contribute to cellular perturbation in this model.     

Use of erythrocyte diagnostic agents in the universal system of serological reactions

A method of parallel serologic studies of the material for the detection of specific antigen or antibodies is proposed. This method is not inferior to the known systems of serologic tests (passive hemagglutination-antigen neutralization tests, passive hemagglutination--antibody neutralization tests, etc) in sensitivity and economy, but exceeds all of them in informative value. The method has been tested both experimentally and in the epizootic study of plague infection used as a model. A serologic tests with the use of erythrocyte diagnosticums are based on a universal principle, this method may be used for other infections.     

A novel trinucleotide repeat expansion at chromosome 3q26.2 identified by a CAG/CTG repeat expansion detection array

CAG/CTG repeat expansions cause at least 12 different neurological disorders, and additional disorders of this type probably exist. Using the repeat expansion detection (RED) assay, we identified an expanded CAG/CTG repeat in a 50-year-old woman with an autosomal dominant syndrome with prominent progressive sensory neuropathy. The expansion could not be accounted for by any of the CAG/CTG repeats known to undergo expansion. To identify the locus of the expansion, we created a PCR array to assess the repeat length of all repeats of eight or more CAG or CTG triplets in the human genome. The expansion was localized to a repeat contained in an intron of a Genscan-predicted gene, 185 nt downstream of a predicted exon that is conserved through mouse. The closest experimentally verified gene in the region (TNIK, encoding a serine/threonine kinase) occurs approximately 63 Kb downstream from the repeat. The length of the expansion in the proband is 98 triplets. This repeat is not expanded in the proband’s cousin (the only other affected family member for whom DNA is currently available) and no expansions were detected in a set of 230 patients with movement disorders of unknown cause. An expanded allele containing 58 triplets was detected in a single control individual, and no other expansions were detected in a set of 255 controls. The normal repeat length ranges from 5 to 30 triplets, with 8 triplets the most common allele. Our results suggest that this new repeat expansion is probably not the direct cause of the phenotype in the proband. Whether the repeat contributes to the patient’s phenotype, or is associated with another phenotype, remains to be determined.Electronic Supplementary Material Supplementary material is available for this article at .     

A study of the influence of yeast cell debris on protein and alpha-glucosidase adsorption at various zones within the expanded bed using in-bed sampling

Expanded bed adsorption chromatography is used to capture products directly from unclarified feedstocks, thus combining solid-liquid separation, product concentration and preliminary purification into a single step. However, when non-specific ion-exchangers are used as the adsorbent in the expanded bed, there is the possibility that electrostatic interactions of cells or cell debris with the adsorbent may interfere with the adsorption of soluble products. These interactions depend on the particle size of the cell debris and its surface charge, which in turn depend on the extent of disruption used to release the intracellular products. The interactions occurring during expanded bed adsorption between the anionic ion-exchanger STREAMLINE DEAE and particulate yeast homogenates obtained by high pressure homogenisation at different intensities of disruption achieved by operating at different pressures were studied, while maintaining all other parameters constant. In-bed sampling from the expanded bed using ports fitted up the height of expanded bed was used to study the retention of yeast cells and cell debris within the bed and its influence on the adsorption of total soluble protein and alpha-glucosidase within various zones of the expanded bed. The retention of the biomass present in the homogenate obtained at a lower intensity of disruption was found to be high at the lower end of the column (17% from 13.8 MPa sample compared to 1% from 41.4 MPa sample). This interaction of the particulate material with the adsorbent was found to reduce the dynamic binding capacity of the adsorbent for total soluble protein from 3.6 mg/mL adsorbent for 41.4 MPa sample to 3.0 mg/mL adsorbent for 13.8 MPa sample. The adsorption of alpha-glucosidase was found to increase with an increase in the concentration of the enzyme in the feed, which increased with the intensity of disruption. Selective adsorption of 6,732 U alpha-glucosidase per mg of total protein bound, was noticed for the feedstock prepared at a higher disruption intensity at 41.4 MPa compared to adsorption of 1,262 U/mg of total protein bound for that prepared at 13.8 MPa. The selective adsorption of alpha-glucosidase due to its high concentration together with simultaneous high specific activity of the enzyme in the feed indicated the significance of selective release of enzymes during microbial cell disruption for efficient expanded bed adsorption processes.     

Physiological color change in squid iridophores

Evidence is presented that changes in the optical properties of active iridophores in the dermis of the squid Lolliguncula brevis are the result of changes in the ultrastructure of these cells. At least two mechanisms may be involved when active cells change from non-iridescent to iridescent or change iridescent color. One is the reversible change of labile, detergent-resistant proteinaceous material within the iridophore platelets, from a contracted gel state (non-iridescent) to an expanded fluid or sol state when the cells become iridescent. The other is a change in the thickness of the platelets, with platelets becoming significantly thinner as the optical properties of the iridophores change from non-iridescent to iridescent red, and progressively thinner still as the observed iridescent colors become those of shorter wavelengths. Optical change from Rayleigh scattering (non-iridescent) to structural reflection (iridescent) may be due to the viscosity change in the platelet material, with the variations in observed iridescent colors due to changes in the dimensions of the iridophore platelets.     

Hunting and predation in a fiddler crab

Fiddler crabs are known primarily to be deposit feeders. They eat detritus, bacteria, and other small particles of organic material found in the sandy or muddy substrate on which they live. They have highly specialized mouthparts used to separate edible matter from nondigestable material. Here we provide evidence of cannibalism and predation in a fiddler crab, Uca annulipes. We additionally provide the first evidence of a fiddler crab hunting shrimp and insects. This study is an exemplary reminder that, even though an animal may have evolved highly specialized feeding traits, this need not preclude it from opportunistically acting as a generalist feeder.     

Application of LCA as a decision-making tool for waste management systems

Aim, Scope and Background  When materials are recycled they are made available for use for several future life cycles and can therefore replace virgin material more than just once. In order to analyse the optimal waste management system for a given material, the authors have analysed the material flows in a life cycle perspective. It is important to distinguish this approach for material flow analysis for a given material from life cycle analysis of products. A product life cycle analysis analyses the product system from cradle to grave, but uses some form of allocation in order to separate the life cycle of one product from another in cases where component materials are recycled. This paper does not address allocation of burdens between different product systems, but rather focuses on methodology for decision making for waste management systems where the optimal waste management system for a given material is analysed. The focus here is the flow of the given material from cradle (raw material extraction) to grave (the material, or its inherent energy, is no longer available for use). The limitation on the number of times materials can be recycled is set by either the recycling rate, or the technical properties of the recycled material. Main Features  This article describes a mathematical geometric progression approach that can be used to expand the system boundaries and allow for recycling a given number of times. Case studies for polyethylene and paperboard are used to illustrate the importance of including these aspects when part of the Goal and Scope for the LCA study is to identify which waste management treatment options are best for a given material. The results and discussion examine the different conclusions that can be reached about which waste management option is most environmentally beneficial when the higher burdens and benefits of recycling several times are taken into account. Results  In order to assess the complete picture of the burdens and benefits arising from recycling the system boundaries must be expanded to allow for recycling many times. A mathematical geometric progression approach manages to take into account the higher burdens and benefits arising from recycling several times. If one compares different waste management systems, e.g. energy recovery with recycling, without expanding the system to include the complete effects of material recycling one can reach a different conclusion about which waste management option is preferred. Conclusions  When the purpose of the study is to compare different waste management options, it is important that the system boundaries are expanded in order to include several recycling loops where this is a physical reality. The equations given in this article can be used to include these recycling loops. The error introduced by not expanding the system boundaries can be significant. This error can be large enough to change the conclusions of a comparative study, such that material recycling followed by incineration is a much better option than waste incineration directly. Recommendations and Outlook  When comparing waste management solutions, where material recycling is a feasible option, it is important to include the relevant number of recycling loops to ensure that the benefits of material recycling are not underestimated. The methodology presented in this article should be used in future comparative studies for strategic decision-making for waste management. The approach should not be used for LCAs for product systems without due care, as this could lead to double counting of the benefits of recycling (depending on the goal and scope of the analysis). For materials where the material cycle is more of a closed loop and one cannot truly say that recycled materials replace virgin materials, a more sophisticated approach will be required, taking into account the fact that recycled materials will only replace a certain proportion of virgin materials.     

Evaluation of the specificity of lectin binding to sections of plant tissue

Hand sections of young corn root tips have been used in a study of problems encountered in the binding of fluorescently-labelled lectins to plant tissues. It was found, surprisingly, that with lectins specific for a sugar known to be present (Lotus and Ulex lectins for L-fucose), with a lectin specific for a sugar thought not to be present (wheat-germ agglutinin for N-acetylglucosamine), with non-lectin glycoprotein and protein (gamma-globulin and bovine serum albumin) and with basophilic dyes (alcian blue and toluidine blue), a coincidental binding pattern similar to the pattern of autofluorescence in the same tissue was obtained. Corn root tissues include cell walls composed of complex polysaccharides esterified with ferulic acid residues, as well as mucilages which are highly hydrated and expanded. In such material, neither standard inhibition controls with haptens nor the use of a wide range of lectin concentrations are adequate to distinguish clearly specific and non-specific binding of fluorescently-labelled lectin. Therefore, lectins are not the simple test probes they have been supposed. Before interpreting results obtained in using fluorescently-labelled lectins on any tissue sections, all available information (biochemical as well as histochemical) about the tissue must be considered.     

Pathologic features of the CHARGE association: support for involvement of the neural crest

Defects associated with choanal atresia include coloboma, cardiac anomalies (usually involving the conotruncal region), physical or mental retardation, genital hypoplasia, and abnormalities of the ear. This constellation of defects is known as the "CHARGE" association and may be accompanied by other anomalies. Many of these defects seem to result from abnormalities in the development, migration, or interaction of cells of the cephalic neural crest. The range of variation in neural crest development is substantial, as indicated by the rather large number of malformation complexes and syndromes that are related phenotypically to the CHARGE association. The increasingly unwieldy nature of this collection of malformations demonstrates the need for an expanded classification of the "neurocrestopathies."     

Studies on the compaction of isolated nucleoids from Escherichia coli

The genomic DNA of Escherichia coli is contained in one or two compact bodies known as nucleoids. Isolation of typically shaped nucleoids requires control of DNA expansion, accomplished here by a modification of the polylysine-spermidine procedure. The ability to control expansion of in vitro nucleoids has application in nucleoid purification and in preparation of samples for high-resolution imaging, and may allow an increased resolution in gene localization studies. Polylysine of relatively low average molecular weight (approximately 3 kDa) is used to produce lysates containing nucleoids that are several-fold expanded relative to the sizes of in vivo nucleoids. These expanded forms can be converted to compact forms similar in dimensions to the cellular nucleoids by either a further addition of polylysine or by incubation of diluted lysates at 37 degrees C. The incubation at 37 degrees C is accompanied by autolytic degradation of most ribosomal RNA. Hyperchromism and circular dichroism spectra indicate that polylysine-DNA complexes are modified during the incubation. Compact forms of the nucleoid can be progressively reexpanded by exposure to salt solutions. Nucleoid compaction was similar in lysates made from rapidly or slowly growing cells or from cells that had been briefly treated with chloramphenicol to reduce linkages between DNA and cell envelope.     

Static indentation of anisotropic biomaterials using axially asymmetric indenters--a computational study

Indentation has historically been used by biomechanicians to extract the small strain elastic or viscoelastic properties of biological tissues. Because of the axisymmetry of indenters used in these studies however, analysis of the results requires the assumption of material isotropy and often yields an "effective" elastic modulus. Since most biological tissues such as bone and myocardium are known to be anisotropic, the use of conventional indentation techniques for estimating material properties is therefore limited. The feasibility of using an axially asymmetric indenter to determine material directions and in-plane material properties for anisotropic tissue is explored here using finite element analysis. The load versus displacement curves as would be measured by an indenter depend on the orientation of the indenter cross section relative to the in-plane material axes, thus suggesting a method for determining the underlying material directions. Additionally, the stiffness of the tissue response to indentation is sensitive to the values of the in-plane anisotropic material properties and prestretches, and thus test results can be used to back out relevant constitutive parameters.     

A new species of Deinsdorfia (Soricidae, Insectivora, Mammalia) from the Pliocene of Spain

A new species of Deinsdorfia is defined using new material coming from the karstic fissure infilling of Almenara-Casablanca 4 (Castelló, Spain), which shows important differences with the rest of the previously known species of the genus. The definition of a new species is supported by the characters found in extra material coming from the localities of Valdeganga, in the Albacete Province (Spain). The stratigraphical occurrence of this genus of pigmented-toothed shrews reinforces the idea of the Iberian Peninsula as a sink area during the Pliocene, where some Central-European soricids expanded their distribution. Most of those migrations or distributional expansions coincide with moments of climatic changes in the northern hemisphere.     

The progenitor cell inhibition assay to measure the anti-leukemic reactivity of T cell clones against acute and chronic myeloid leukemia

Adoptive immunotherapy with donor T lymphocytes may be used as a treatment for relapsed leukemia after allogeneic hematopoietic stem cell transplantation (SCT). In vitro selected and expanded anti-leukemic T cells may be more effective in inducing a response in vivo. To identify the anti-leukemic reactivity of in vitro generated T cells, standard target cell read-out assays like the 51Cr-release assay are not always appropriate. We developed an assay in which the ability of T cells to antigen specifically inhibit the in vitro growth of leukemic progenitor cells in the presence of cytokines can be measured. This assay allows the evaluation of the cytolytic or suppressive potential of leukemia reactive T cells for prolonged periods of time. The assay is based on inhibition of [3H]thymidine incorporation by the leukemic progenitor cells induced by multiple hematopoietic growth factors. T cell clones with a known specificity were used to compare the analytic potential of the new assay with those of other cytotoxicity assays. Based on the results of the T cell clones, a modification of a limiting dilution assay was developed to identify anti-leukemic allogeneic T cells in HLA identical donor-recipient combinations selected on their ability to inhibit the in vitro growth of CML or AML progenitor cells, to be used for the generation of leukemia-reactive CTL lines for clinical use.     

Industrial Ecosystems and Food Webs: An Expansion and Update of Existing Data for Eco‐Industrial Parks and Understanding the Ecological Food Webs They Wish to Mimic

Cyclical industrial networks are becoming highly desirable for their efficient use of resources and capital. Progress toward this ideal can be enhanced by mimicking the structure of naturally sustainable ecological food webs (FWs). The structures of cyclic industrial networks, sometimes known as eco‐industrial parks (EIPs), are compared to FWs using a variety of important structural ecological parameters. This comparison uses a comprehensive data set of 144 FWs that provides a more ecologically correct understanding of how FWs are organized than previous efforts. In conjunction, an expanded data set of 48 EIPs gives new insights into similarities and differences between the two network types. The new information shows that, at best, current EIPs are most similar to those FWs that lack the components that create a biologically desirable cyclical structure. We propose that FWs collected from 1993 onward should be used in comparisons with EIPs, given that these networks are much more likely to include important network functions that directly affect the structure. We also propose that the metrics used in an ecological analysis of EIPs be calculated from an FW matrix, as opposed to a community matrix, which, to this point, has been widely used. These new insights into the design of ecologically inspired industrial networks clarify the path toward superior material and energy cycling for environmental and financial success.     

Use of combinatorial peptide libraries for T-cell epitope mapping

T lymphocytes play important roles not only in infectious diseases and autoimmunity, but also in immune responses against tumors. For many of these disorders, the relevant target antigens are not known. Designing effective methods that allow the search for T-cell epitopes is therefore an important goal in the areas of infectious diseases, oncology, vaccine development, and numerous other biomedical specialties. So far, the strategies used to examine T-cell recognition have been based largely on mapping T-cell epitopes with overlapping peptides from known proteins or with entire proteins, e.g., from a specific virus, bacterium, or human tissue. These approaches are tedious and have a number of limitations. It is, for example, almost impossible to isolate T cells that infiltrate an organ or infectious site and identify their specificity unless one already has a concept as to which antigens may be relevant. During recent years, a number of laboratories have developed less biased approaches that employ either the selection of putative T-cell epitopes based on the prediction of binding to certain major histocompatibilty complex (MHC) molecules and peptide or protein libraries that have been generated in expression systems, e.g. phage, or rely on combinatorial peptide chemistry. The latter technique has been refined by a number of laboratories including ours. Bead-bound or, preferably, positional scanning synthetic and soluble combinatorial peptide libraries allow the identification of T-cell epitopes within complex mixtures of proteins even for T cells that have been expanded from an organ infiltrate with a polyclonal stimulus. The practical steps that are involved in the latter method are described in this article.     

DMSO and glycerol reduce bacterial death induced by expression of truncated N-terminal huntingtin with expanded polyglutamine tracts

Huntington's disease (HD) is caused by CAG repeat expansion in exon 1 of a large gene, IT15, possessing 67 exons. Transgenic mice expressing a truncated N-terminal peptide of huntingtin with an expanded polyglutamine tract translated only from exon 1 develop symptoms similar to Huntington's disease. In the present study, a bacterial system (Escherichia coli) was used to express truncated peptides of huntingtin translated from exon 1 of the HD gene. Bacterial death was observed after the induction of peptides with expanded polyglutamine tracts, and both sodium dodecyl sulfate (SDS)-soluble peptides and insoluble aggregated material were detected by immunoblotting in the homogenates of such E. coli. E. coli death was partially reduced by the addition of dimethylsulfoxide (DMSO) or glycerol to the medium, with a consequent decrease in aggregated material and an increase in SDS-soluble peptide in the homogenate. These results suggest that DMSO and glycerol may decrease the toxicity of huntingtin with expanded polyglutamine tracts by acting as chemical chaperones.