Genome specific,highly repeated sequences of Hordeum vulgare: cloning,sequencing and squash dot test

Summary Highly repeated sequences of nuclear DNA from barley Hordeum vulgare (L.) variety Erfa were cloned. Several clones containing barley specific repeated DNA were analysed by sequence analysis and Southern blot hybridization. The investigated repeats differ from each other in their length, sequence and redundancy. Their length ranges from 36 bp to about 180 bp. The repeats are AT-rich and differ widely in their redundancy within the barley genome. Southern analysis showed that the repeats belong to different repetition complexes. The possibility for utilizing these clones as probes for simple and fast genome analysis is demonstrated in squash dot experiments.     

Multi-element analysis of the rat hippocampus by proton induced X-ray emission spectroscopy (phosphorus,sulphur, chlorine,potassium, calcium,iron, zinc,copper, lead,bromine, and rubidium)

Summary A technique for multi-element analysis of brain tissue by proton induced X-ray emission spectroscopy (PIXE) is described and data from analysis of fixed and unfixed samples from rat hippocampus, neocortex, amygdala, and spinal cord is presented and commented on. The atoms present in the tissue are bombarded with protons which causes the ejection of electrons from the inner shells. When the holes are refilled with electrons from outer shells, X-ray quanta characteristic for each element are emitted. Using a high resolution energy dispersive detector a complete X-ray spectrum of the specimen can be recorded in a single measurement. Detection limits 5 p.p.m. of dry matter are obtained for most elements with atomic number >14 (silicon). Around 13 elements were found in concentrations above the detection limits. The grand means for non-fixed hippocampi were e.g. for Zn–120 p.p.m.; Rb–20 p.p.m.; Fe–150 p.p.m.; Pb–3 p.p.m.; Ni–5 p.p.m.     

Glycogen phosphorylase in Dictyostelium discoideum: demonstration of two developmentally regulated forms, purification to homogeneity, immunochemical analysis, cAMP induction, in vitro translation, and molecular cloning

A key step in the cellular differentiation of Dictyostelium is the degradation of glycogen to provide the precursors for synthesis of the structural end products of development. We have found that the enzyme that initiates this degradative pathway, glycogen phosphorylase (1,4-alpha-D-glucan:orthophosphate alpha-glucosyltransferase; EC 2.4.1.1), is developmentally regulated and exists as two forms. During the time course of development, a previously undescribed activity, the "b" form, decreases, while that of the "a" form increases. The "b" form is inactive unless 5'AMP is included in the reaction mixture. The two forms differ in their elution from DE52 cellulose, affinity constants, thermal stability, affinity for 5'AMP Sepharose, subunit molecular weight, and peptide maps. In crude extracts, anti-a antiserum stains a 104-kD protein that is associated with phosphorylase "a" activity and appears late in development, while anti-b antiserum stains a 92-kD protein that is associated with phosphorylase "b" activity and is present throughout development. We have also demonstrated in vitro phosphorylation of the "b" form by an endogenous protein kinase and a corresponding loss of 5'AMP dependence. If intact cells were exposed to exogenous cAMP, "b" activity decreased and was replaced by "a" activity, as well as the 104-kD protein band on SDS-PAGE. In order to determine if the two forms of the enzyme are different gene products, we screened lambda gt11 expression libraries with antibodies against the purified "a" and "b" forms. Three clones were found to be overlapping by Southern analysis. A yeast glycogen phosphorylase cDNA clone (gpy) and a human muscle glycogen phosphorylase clone (HM-11) cross-hybridized with the Dictyostelium inserts, and gpy shared a few common restriction fragments with the Dictyostelium clones on genomic blots. Northern analysis of Dictyostelium total RNA showed that the Dictyostelium inserts and gpy recognize an mRNA of 3.2 kb, while on poly A-enriched RNA, the yeast clone detects preferentially a 3.6-kb message.     

Unit activities of the salmon Salmo salar preoptic nucleus in Parr, Parr-Smolt and Smolt stadia]

The olfactory and gustatory stimulations with NaCl (10(-5)-10(-2) M/1) bring about certain typical modifications of the preoptic cells activity in the case of "Parr" and "Parr smolt". The "on" or "off" or "on and off" effects are very marked. Unlike the "Smolt" stage is accompanied by an important decrease of the preoptic cells activity, sometimes until complete silence of the nucleus. Data analysis: sequential analysis and statistical analysis. The activities recorded on a magnetic tape are feld to a mini computer.     

Morphological basis of "growling" in the king cobra, Ophiophagus hannah.

A bioacoustic analysis is conducted on the defensive sounds produced by 21 species of snakes. The "typical" snake hiss is described as having a broad-frequency span (from roughly 3,000 to 13,000 Hertz) and a dominant frequency near 7,500 Hertz. The "growl" of the king cobra (Ophiophagus hannah) differs from the "typical" snake hiss in consisting solely of frequencies below 2,500 Hertz, with a dominant frequency near 600 Hertz. Structural analysis of the upper respiratory tract of O. hannah suggests that the "growl" is produced by tracheal diverticula functioning as low-frequency resonating chambers. This hypothesis is supported in several ways. An acoustic analysis of a mechanical model of the trachea demonstrates the potential for these diverticula to produce resonance effects. A "growl" also occurs in the mangrove ratsnake (Gonyosoma oxycephalum), a species that also has tracheal diverticula. Flushing the respiratory tract of G. oxycephalum with helium produces a shift of over 1,000 Hertz in the "growl," a shift that is indicative of a resonance effect.     

Comparative environmental assessment of conventional,electric, hybrid,and fuel cell powertrains based on LCA

Purpose

The purpose of this study is to compare the environmental impact differences of four types of vehicles on a life cycle assessment (LCA) perspective: a conventional gasoline vehicle, a pure electric vehicle, a plug-in hybrid gasoline-electric vehicle, and a plug-in hybrid fuel cell-battery vehicle. The novelty of the approach is to consider the different powertrains—electric and hybrids—as a repowering of the conventional powertrain. This way, the attention can be focused only on the powertrain differences and inefficiencies, with the added value of avoiding further assumptions, which could cause the analysis to be somehow rough.

Methods

Thus, we compared four powertrain scenarios maintaining the same vehicle chassis, and we compared the impacts from the powertrain production, vehicle use phase, and powertrain end of life only. Hence, special attention was paid to the inventory for powertrain construction and use phase. For the powertrain components, an accurate literature survey has been carried out for the life cycle inventory. For the use phase, several driving cycles, both standardized and real-world type, have been simulated in order to properly evaluate the effect on the fuel/electricity consumption. For the comparison, environmental indicators according to cumulative energy demand (CED) and ReCiPe Midpoint methods have been used. This way, an analysis of the environmental impact, based on a life cycle impact assessment approach, is provided, which allows thoroughly comparing the systems based on the different powertrains. Moreover, a sensitivity analysis on different energy mixes has been included, which represents also a way to take into account changes in electricity production.

Results and discussion

Results are presented according to life cycle impact assessment, which examines the mass and energy inventory input and output data for a product system to translate these data to better identify their possible environmental relevance and significance. In the case of the climate change (CC), fuel depletion (FD), and CED indicators, the lowest value corresponds to the plug-in hybrid gasoline-electric vehicle, followed by the plug-in hybrid fuel cell-battery vehicle, the pure electric, and finally the conventional gasoline vehicle. Substituting a conventional gasoline powertrain with the corresponding pure electric one offers the lowest reduction, but still of valuable amount. In our analysis, for the considered systems, the reduction of the value of CC is about 15%, the reduction of the value of CED is about 12%, and the reduction of FD value is about 28%. This analysis underlines the weakness of a tank-to-wheel comparison, according to which the pure electric powertrain, having a very high average efficiency, results in being the less consuming, followed by the hybrid gasoline-electric and fuel cell-battery vehicles, respectively, and then by the conventional vehicle. Instead, in terms of CED, the bad influence of the low average efficiency of the Italian electricity production is highlighted. The LCA approach also stresses out the importance of the battery inventory, which can make the environmental performance of the system based on the pure electric vehicle significantly worse than those based on the conventional vehicle. Of a great significance is the presence of a group of indicators—including human toxicity, eutrophication, and acidification—with lower values in the case of conventional gasoline vehicle than in the electric and hybrid ones, which further confirms that the potential of electrified vehicles strictly depends on an efficient production and recycling of the battery.

Conclusions

The analysis underlines an alarming list of environmental impact indicators, usually neglected, which are worsened by the powertrains electrification. Operating on the production processes, used materials and recycling phase can possibly mitigate these worsening effects. Also, the type of electricity is shown to strongly affect the results. Thus, performing specific evaluations for different countries is crucial and a sensitivity analysis, involving drastically different energy mixes, can allow for taking into account possible changes in the future electricity production.

     

Super-motifs and evolution of tandem leucine-rich repeats within the small proteoglycans--biglycan, decorin, lumican, fibromodulin, PRELP, keratocan, osteoadherin, epiphycan, and osteoglycin

Leucine-rich repeats (LRRs) with 20-30 amino acids in unit length are present in many proteins from prokaryotes to eukaryotes. The LRR-containing proteins include a family of nine small proteoglycans, forming three distinct subfamilies: class I contains biglycan/PG-I and decorin/PG-II; class II: lumican, fibromodulin, PRELP, keratocan, and osteoadherin; and class III: epiphycan/PG-Lb and osteoglycin or osteoinductive factor. Comparative sequence analysis of the 34 available protein sequences reveals that these proteoglycans have two types of LRRs, which we call S and T. The type S LRR is 21 residues long and has the consensus sequence of xxaPzxLPxxLxxLxLxxNxI. The type T LRR has 26 residues; its consensus sequence is zzxxaxxxxFxxaxxLxxLxLxxNxL. In both "x" indicates variable residue; "z" is frequently a gap; "a" is Val, Leu, or Ile; and I is Ile or Leu. These type S and TLRRs are ordered into two super-motifs--STT with about 73 residues in classes I and II and ST with about 47 residues in class III. The 12 LRRs in the small proteoglycans of I and II are best represented as (STT)4; the seven LRRs of class III as (ST)T(ST)2. Our analyses indicate that classes I/II and III evolved along different paths after the establishment of the precursor ST, and classes I and II also diverged after the establishment of the precursor (STT)4.     

Signifying the Pandemics: Metaphors of AIDS, Cancer, and Heart Disease

This article offers a symbolic analysis of the cultural construction and signification of three of the major "pandemics" of the late 20th century: AIDS, cancer, and heart disease. It is based on unstructured interviews conducted in Israel between 1993–94 with 75 nurses and 40 physicians and between 1993–95 with 60 university students. Two key symbols, "pollution" and "transformation" are shown to constitute AIDS and cancer within a symbolic space that I suggest is "beyond culture" where body boundaries are dissolved and cultural categories are dismantled. Heart disease, in contrast, is metaphorized as a defect in the "body machinery." The article concludes by arguing that heart attack is depicted as the pathology of the Fordist, modernist body, while AIDS/cancer are pathologies of the postmodern body in late capitalism. [AIDS, cancer, heart disease, semiotics, metaphorization]     

Neuroimaging of cognition: past, present, and future

Neuroimaging, particularly that based upon functional magnetic resonance (fMRI), has become a dominant tool in cognitive neuroscience. This review provides a personal and selective perspective on its past, present, and future. Two trends currently characterize the field that broadly reflect a pursuit of "where"- and "how"-type questions. The latter addresses basic mechanisms related to the expression of task-induced neural activity and is likely to be an increasingly important theme in the future. This trend entails an enhanced symbiosis among investigators pursuing similar questions in fields such as computational and theoretical neuroscience as well as through the detailed analysis of microcircuitry.     

Transthyretin Pro55, a variant associated with early-onset,aggressive, diffuse amyloidosis with cardiac and neurologic involvement

Summary Mutations in the protein transthyretin cause amyloidosis involving the heart, peripheral nerves, and other organs. A family from West Virginia developed an unusually aggressive form of widespread transthyretin amyloidosis. Single-strand conformation polymorphism analysis revealed a variant in the transthyretin gene, which was found on sequencing to be a TC transversion at position 2 of codon 55, corresponding to a Leu Pro substitution. The variant sequence was confirmed by restriction analysis and polymerase chain reaction (PCR)-primer introduced restriction analysis.     

Logical, epistemological and statistical aspects of nature-nurture data interpretation

In this paper the nature of the reasoning processes applied to the nature-nurture question is discussed in general and with particular reference to mental and behavioral traits. The nature of data analysis and analysis of variance is discussed. Necessarily, the nature of causation is considered. The notion that mere data analysis can establish "real" causation is attacked. Logic of quantitative genetic theory is reviewed briefly. The idea that heritability is meaningful in the human mental and behavioral arena is attacked. The conclusion is that the heredity-IQ controversy has been a "tale full of sound and fury, signifying nothing". To suppose that one can establish effects of an intervention process when it does not occur in the data is plainly ludicrous. Mere observational studies can easily lead to stupidities, and it is suggested that this has happened in the heredity-IQ arena. The idea that there are racial-genetic differences in mental abilities and behavioral traits of humans is, at best, no more than idle speculation.     

Vectorial capacity, basic reproduction number, force of infection and all that: formal notation to complete and adjust their classical concepts and equations

A dimensional analysis of the classical equations related to the dynamics of vector-borne infections is presented. It is provided a formal notation to complete the expressions for the Ross' Threshold Theorem, the Macdonald's basic reproduction "rate" and sporozoite "rate", Garret-Jones' vectorial capacity and Dietz-Molineaux-Thomas' force of infection. The analysis was intended to provide a formal notation that complete the classical equations proposed by these authors.     

Diversity, geographical distribution, and conservation of Cactaceae in the Mier y Noriega region, Mexico

We carried out an inventory of the cactus species occurring in the Mier y Noriega region. The study was conducted in a square-shaped area of approximately 2845km², located in the southeastern segment of the Chihuahuan Desert region, between 23°00 – 23°30 lat. N and 100°00 – 100°30 long. W, including parts of the states of Nuevo León, Tamaulipas, and San Luis Potosí, Mexico. In order to know the cactus diversity, we developed an intensive method of botanical collecting; a total of 80 sites were sampled. With 54 species recorded, of which 28 were new area records and 14 new state records, the Mier y Noriega region is considered moderately rich in cactus species. Cactus diversity is distributed unevenly in the area, and the greatest species concentration occurs in its southwestern portion. The analysis of geographical distribution of individual species showed that the highest proportion (82%) are endemic to the Chihuahuan Desert Region, six of them having extremely narrow distributions. In addition, 19 species are considered endangered. With the aid of a complementarity analysis, we propose a strategy for the optimal conservation of the species and their habitats.     

Altruism, Altruistic Punishment and Social Investment

The concept of altruism is used in very different forms by computer scientists,economists, philosophers, social scientists, psychologists and biologists. Yet, in order to be useful in social simulations, the concept "altruism" requires a more precise meaning. A quantitative formulation is proposed here, based on the cost/benefit analysis of the altruist and of society at large. This formulation is applied in the analysis of the social dynamic working of behaviors that have been called "altruistic punishments", using the agent based computer model Sociodynamica. The simulations suggest that "altruistic punishment" on its own cannot maintain altruistic behaviors. "Altruistic behavior" is sustainable in the long term only if these behaviors trigger synergetic forces in society that eventually make them produce benefits to most individuals. The simulations suggest however that "altruistic punishment" may work as a "social investment", and is thus better called "decentralized social punishment". This behavior is very efficient in enforcing social norms. The efficiency of decentralized social punishment in enforcing norms was dependent on the type of labor structured of the virtual society. I conclude that what is called "altruistic punishment" emerges as a type of social investment that can evolve either through individual and/or group selection, as a successful device for changing or enforcing norms in a society. Social simulations will help us in better understanding the underlying dynamic working of such devices.     

The diet transform of lattice patterns,equivalence relations,and similarity measures

The diet algorithm is introduced for the reduction of square-cell lattice patterns to simpler graphs that contain fewer C ₄ cells. By repeated applications of the algorithm, the lattice pattern is converted into a graph representing the skeletal structure of the pattern. Based on the algorithm, equivalence relations and dissimilarity measures are introduced for lattice patterns, providing tools for shape analysis of planar patterns, such as projections of molecular contour surfaces used in molecular design. This algorithm is applied to a series of examples, illustrating the features of the method.     

Detection of RFLP markers associated with antibody response in meat-type chickens: haplotype/genotype, single-band, and multiband analyses of RFLP in the major histocompatibility complex

Improving disease resistance in poultry by direct selection or by selecting for immune response is hardly feasible due to the quantitative nature of these traits, their low heritability, and the difficulties associated with reliable measurements. In this situation, marker-assisted selection (MAS) is expected to be a more effective breeding approach. The major histocompatibility complex (MHC), known to affect immune response and disease resistance, was examined as a set of candidate genes for association between DNA markers and antibody response. Backcross (BC1) and F2 families were generated from a cross between lines divergently selected for high or low antibody response to Escherichia coli vaccination. Restriction fragment length polymorphism (RFLP) analysis of the highly polymorphic MHC class IV (B-G) region suggested an association with antibody response to several antigens (E. coli, SRBC, NDV). The multiband data generated with the class IV probe were used to compare the efficacies of three alternative analyses: "single-band" (carriers versus noncarriers of each RFLP band separately), "multiband" (multiple regression on all RFLP bands), and "genotype" (determined from family analysis of RFLP patterns/haplotypes). Groups of birds identified by the "multiband" analysis were identical to the haplotype-based genotypes, suggesting that the laborious step of haplotype determination can be omitted without unduly sacrificing power of analysis.     

Genetic characteristics of the "EEC" syndrome (ectrodactyly, ectodermal dysplasis, cheilognathopalatoschisis)]

The analysis of the literature and author's observations of the "EEC" syndrome (ectrodactyly, ectodermal dysplasia and cleft lip/palate) revealed that this is a disorder with an autosomal-dominant type of inheritance with an incomplete penetrance and varying expressivity. Both sexes are affected with the same frequency. The complete form of the syndrome was mentioned in 27 cases only; all other patients had incomplete forms. The combination of two out of 3 main features is enough for the diagnosis of this syndrome. The most common trait of the "EEC" syndrome is ectrodactyly (73/77), clefts of lip or palate were observed in 53 patients out of 77, the ectodermal dysplasia was mentioned in 44 cases. There is an increase of mutation frequency in older parents.     

Status of Corynosoma (Acanthocephala: Polymorphidae) based on anatomical, ecological, and phylogenetic evidence, with the erection of Pseudocorynosoma n. gen

The possession of genital spines has been considered as a key taxonomic trait to differentiate Corynosoma from other genera of the Polymorphidae. However, Corynosoma currently consists of 2 groups of species with clear ecological and morphological divergences: the "marine" group (with ca. 30 species) infects mammals and piscivorous birds in the marine realm, whereas the "freshwater" group (with ca. 7 species) infects waterfowl in continental waters. Species from these groups differ in shape of body and neck, trunk spination, lemnisci length and shape, testes arrangement, and number and shape of cement glands. We tested whether species from these 2 groups formed a monophyletic assemblage based on a phylogenetic analysis by using 15 morphological characters. We also included species of Andracantha, Polymorphus, and Hexaglandula with which potential taxonomic conflicts could most likely arise. We obtained 108 equally most parsimonious trees of 32 steps, with a consistency index (CI) = 0.59, and a retention index (RI) = 0.82. The strict consensus tree indicated that the "freshwater" species of Corynosoma form a monophyletic assemblage closely related to some species of Polymorphus, whereas the "marine" species of Corynosoma are grouped together with Andracantha. Accordingly, Corynosoma is not a monophyletic assemblage, and Pseudocorynosoma n. gen. is proposed for the "freshwater" species of Corynosoma. This decision was strongly supported by (1) a functional comparison of foretrunk muscles between species of Polymophus, Andracantha, and Corynosoma; (2) a multivariate morphometric study of proboscis characters and egg size; and (3) an analysis of ecological patterns of host-parasite relationships.