An Analysis of Variance of Nominal Data

This paper considers a common problem in analysis of variance where the responses to a set of treatments are nominal (i.e. are recorded in frequencies) with no underlying metric. Reasoning by analogy from standard analysis of variance of a two-way classification we develop chi-square tests for significance of treatments and interactions. Two tests are proposed for interaction and their asymptotic properties are studied.     

Mechanisms of madness: evolutionary psychiatry without evolutionary psychology

Delusions are currently characterised as false beliefs produced by incorrect inference about external reality (DSM IV). This inferential conception has proved hard to link to explanations pitched at the level of neurobiology and neuroanatomy. This paper provides that link via a neurocomputational theory, based on evolutionary considerations, of the role of the prefrontal cortex in regulating offline cognition. When pathologically neuromodulated the prefrontal cortex produces hypersalient experiences which monopolise offline cognition. The result is characteristic psychotic experiences and patterns of thought. This bottom-up account uses neural network theory to integrate recent theories of the role of dopamine in delusion with the insights of inferential accounts. It also provides a general model for evolutionary psychiatry which avoids theoretical problems imported from evolutionary psychology.     

Molecular cloning and expression of a major surface protein (the 75-kDa protein) of Porphyromonas (Bacteroides) gingivalis in Escherichia coli

A major immunodominant surface protein (the 75-kDa protein) of Porphyromonas (Bacteroides) gingivalis 381 has been purified and its amino-terminal amino acid sequence has been determined. Using oligonucleotide probes corresponding to the sequence, we identified a recombinant plasmid clone carrying a single 4.2-kb BamHI fragment from pUC19 libraries of P. gingivalis. The BamHI fragment transferred to the bacteriophage T7 RNA polymerase/promoter expression vector system produced a slightly larger (77-kDa) protein, a precursor form, immunoreactive to the antibody against the 75-kDa protein, suggesting that the cloned DNA fragment probably carried an entire gene for the 75-kDa protein. Genomic Southern analysis revealed a single copy of the 75-kDa protein gene per genome among all P. gingivalis strains tested, and that no homologous genes are present in other black-pigmented Bacteroides species. These observations suggest that the 75-kDa protein gene may be useful as a specific DNA probe to classify or to detect this organism.     

Biogeographic area relationships of lowland Neotropical rainforest based on raw distributions of vertebrate groups

Hypotheses of the historic biogeography of Neotropical anurans inhabiting lowland forests were generated using Parsimony Analysis of Endemicity. In order to establish comparisons with the biogeographical patterns of other vertebrates, previous cladistic analyses reported in the literature (for lizards and primates) were extended and reanalysed to match the geographical scope of the anuran analysis. Cladistic analysis of the distribution of 335 anuran species at 14 localities showed two regions that form a basal dichotomy: (1) Central America + Choco and (2) Amazon Basin + Brazilian Atlantic Forest. This result is interpreted as the first vicariance event that separated lowland Neotropical rainforests into Cis-Andean (east from the Andes) and Trans-Andean (west from the Andes) areas. Within the Cis-Andean localities, the earliest separation occurred between the Amazon Basin and the Brazilian Atlantic Forest. Within the Amazon Basin, three distinctive clusters are defined: (1) Belem, (2) Guianan Region, and (3) Upper Amazon Basin. Data sets on the distribution of anurans, lizards, and mammals have strong cladistic signal. Strong congruence exists among the area cladograms of anurans, lizards, and primates. All of them have, or at least did not conflict with: (1) a basal separation between Cis- and Trans-Andean regions, (2) a Central American clade, (3) the Choco Region is sister to the Central American clade, (4) an Amazon Basin clade, (5) an Upper Amazon Basin clade, and (6) a Guianan clade. The area cladograms are dichotomous and therefore do not support biogeographic theories that hypothesize simultaneous isolations of biotas in the Neotropics.     

Vegetation establishment in post-fire Adenostoma chaparral in relation to fine-scale pattern in fire intensity and soil nutrients

At fine spatial scales (0.1–10m), chaparral communities have been shown to be strongly influenced by canopy-gap patterns, leading to periodicities in vegetation at 4–5 m spatial scales. Fine-scale variations in fire behavior and post-fire erosion can lead to changes in the patterning of viable seeds and nutrients and may alter the spatial patterning of post-fire chaparral communities. This study deals with the relationship among fire behavior, post-fire nutrient availabilities and vegetation patterns in a 1-yr old, post-fire Adenostoma fasciculatum chaparral community in the Sierra Nevada Mountains, California, USA. Variations in mineral soil exchangeable cations (Ca, Mg) and extractable phosphorus (P0₄-P) were correlated with ash distribution. Cations and measures of ammonium and nitrate were also correlated with fire intensity, measured by the diameter of the smallest remaining A. fasciculatum twigs following fire. Fire intensity was correlated with the pattern of post-fire vegetation establishment based on first axis DC A scores. However, ash PO4-P was more highly correlated with sample DCA scores, local species richness and total cover (p < 0.01), suggesting that small-scale variations in PO4-P which correlate with ash distributions may be important in structuring this community. Two- and three-term local variance analysis revealed a maximum of pattern intensity in DCA first axis scores at 4–5 m intervals that likely corresponds to pre-fire canopy-gap patterns. However, total cover showed pattern at spatial scales of 8–10 m, and was correlated at this scale with patterns of ash distribution and fire intensity. Microtopographic patterns also occur at similar spatial scales. Microtopographic patterns appear important in determining post-fire plant nutrient and water distributions and, thereby, patterns of plant establishment. Thus, the scale and intensity of post-fire vegetation pattern may differ considerably from pre-fire conditions.     

A new brittle star (Ophiuroidea: Ophiodermatina) from the Early Triassic Paris Biota (Bear Lake County,Idaho, USA)

Knowledge on the morphology of Early Triassic ophiuroids is very limited, in spite of the relatively high number of described species. This hampers attempts to use morphology-based phylogenetic analyses in order to explore the early diversification of the ophiuroid modern clades between the latest Paleozoic and the early Mesozoic. Here, a new ophiuroid from the Early Triassic of southern Idaho (USA) is described and assigned to the new taxon Shoshonura brayardi Thuy nov. gen., nov. sp. It is part of an exceptional Early Triassic faunal assemblage recently described as the Paris Biota. On account of the arm morphology and the shape of the arm spines and arm spine articulations, Shoshonura brayardi nov. gen., nov. sp. is considered a basal member of the suborder Ophiodermatina.     

Comparative study of the antioxidant activity of the essential oils of five plants against the H2O2 induced stress in Saccharomyces cerevisiae

The purpose of this work was to investigate the protective effect of five essential oils (EOs); Rosmarinus officinalis, Thymus vulgaris, Origanum compactum Benth., Eucalyptus globulus Labill. and Ocimum basilicum L.; against oxidative stress induced by hydrogen peroxide in Saccharomyces cerevisiae. The chemical composition of the EOs was analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC/MS). The in vitro antioxidant activity was evaluated and the protective effect of EOs was investigated. Yeast cells were pretreated with different concentrations of EOs (6.25–25 µg/ml) for an hour then incubated with H₂O₂ (2 mM) for an additional hour. Cell viability, antioxidants (Catalase, Superoxide dismutase and Glutathione reductase) and metabolic (Succinate dehydrogenase) enzymes, as well as the level of lipid peroxidation (LPO) and protein carbonyl content (PCO) were evaluated. The chemical composition of EOs has shown the difference qualitatively and quantitatively. Indeed, O. compactum mainly contained Carvacrol, O. basilicum was mainly composed of Linalool, T. vulgaris was rich in thymol, R. officinalis had high α-Pinene amount and for E. globulus, eucalyptol was the major compound. The EOs of basil, oregano and thyme were found to possess the highest amount of total phenolic compounds. Moreover, they have shown the best protective effect on yeast cells against oxidative stress induced by H₂O₂. In addition, in a dose dependent manner of EOs in yeast medium, treated cells had lower levels of LPO, lower antioxidant and metabolic enzymes activity than cells exposed to H₂O₂ only. The cell viability was also improved. It seems that the studied EOs are efficient natural antioxidants, which can be exploited to protect against damages and serious diseases related to oxidative stress.     

An update on carbonic anhydrase-related proteins VIII,X and XI

The catalytically inactive isoforms of carbonic anhydrase (CAs) are known as CA-related proteins (CARPs) VIII, X, and XI. They have highly conserved amino acid sequences. These proteins are predominantly expressed in human and mouse brain, however, their precise roles are poorly known. CARP VIII is functionally associated with motor coordination in human and mouse. CARP X is more highly expressed in the pineal gland during night compared to the day time, suggesting a function for wake/sleep patterns. Phylogeny shows that CARP XI has emerged from CARP X. It is only found in tetrapods and is highly expressed in the central nervous system (CNS) of humans and is also associated with several cancers. Detailed analysis of CARPs is in progress in our laboratory to understand their role in normal physiology. We present a review of literature on CARPs and present some novel data on CARPs obtained in our laboratory.