The Autocovariance Function for Marked Point Processes: A Comparison between Two Different Approaches

Exploratory analysis of marked point patterns has previously been conducted using two disjoint techniques, namely the mark correlation function and spectral analysis. Our purpose here is to present two alternative autocovariance estimators to the mark correlation function which not only apply in both planar and lattice situations, but which in the lattice case can also be considered in terms of the inverse Fourier transform of the spectrum. Moreover, they can be applied to isotropic or anisotropic marked point patterns. Various examples are presented to show how these estimators perform when applied to data sets possessing different kinds of mark structure, and a rank test procedure is proposed to enable the construction of empirical tests of hypothesis.     

The effect of Walker-256 tumour development upon Kupffer cell metabolism

The liver plays a central role in the establishment and maintenance of the cachectic state in rats bearing extra-hepatic tumours. Kupffer cells, which as macrophages, show a strong relationship between metabolism and function could be involved in the alterations observed in the disruption of many functions of the organ as a whole. To assess whether the metabolic/functional pattern of Kupffer cells was altered by cachexia we have investigated the utilization of glucose, glutamine and palmitate by the cells from tumour-bearing and control rats. We have found an enhanced utilization of the three substrates by the cells from tumour-bearing rats as compared with controls, which was related to greater energy production through the Krebs cycle and enhanced production of precursors for the synthesis of the many substances the cells secrete when activated. The use of palmitate as substrate was also augmented in these cells, in the opposition to the observation in stimulated peritoneal macrophages. The availability of palmitate however, was not associated with a reduction of glucose or glutamine consumption. The cycle of interconversion, free fatty acids/triacyglycerol in Kupffer cells from tumour-bearing rats was also found to be increased, as was hydrogen peroxide production. Taken together the results suggest an increased utilization of substrates for both energy production and for synthetic processes (e.g. NADPH for hydrogen peroxide production). © 1998 John Wiley & Sons, Ltd.     

X-ray structures of new dipeptide taste ligands

The molecular basis of sweet taste was investigated by carrying out the crystal state conformational analysis by X-ray diffraction of the following dipeptide taste igands:N-3,3-dimethylbutyl-aspartyl-phenylalanine methyl ester, I (N-DMB-Asp-Phe-OMe), its sodium salt (N-DMB-Asp-Phe-ONa), II , aspartyl-D -2-aminobutyric acid-(S)-α-ethylbenzylamide, III (Asp-D -Abu-(S)-α-ethylbenzylamide), aspartyl-N′-((2,2,5,5-tetramethylcyclopentanyl)-carbonyl)-(R)-1,1-diamino-ethane, IV (Asp-(R)-gAla-TMCP), and aspartyl-D -valine-(R)-α-methoxymethylbenzyl amide, V (Asp-D -Val-(R)-α-methoxymethylbenzylamide). With the exception of the sodium salt II , all compounds are sweet-tasting, showing in some cases considerable potency enhancement with respect to sucrose. The results of this study confirm the earlier model that an ‘L-shape’ molecular array is essential for eliciting sweet taste for dipeptide-like ligands. In addition, it was established that (i) substitution of the N-terminal group does not inhibit sweet taste, if its zwitterionic character is maintained; (ii) a hydrophobic group located between the stem and the base of the L-shape could be responsible for sweetness potency enhancement, as found in I, III and IV ; in fact, the extraordinary potency of the N-alkylated analogue I would support a model with an additional hydrophobic binding domain above the base of the ‘L’; (iii) removal of the methyl ester at the C-terminus of compound I with the salt formation gives rise to the tasteless compound II ; (iv) for the first time all possible side-chain conformers (g⁻,g⁺andt) for the N-substituted aspartyl residue were observed; and (v) a retro-inverso modification, incorporated at position 2 of the dipeptide chain, confers greater flexibility to the molecule, as demonstrated by the contemporary presence of six conformationally distinct independent molecules in the unit cell and yet sweet taste properties are maintained, as found in IV . © 1998 European Peptide Society and John Wiley & Sons, Ltd.     

Helical screw sense of peptide molecules: The pentapeptide system (Aib)4/L-Val[L-(αMe)Val] in the crystal state

The crystal-state preferred conformations of six N^α-blocked pentapeptide esters, each containing four helicogenic, achiral α-aminoisobutyric acid (Aib) residues followed by one chiral L -valine (L -Val) or C^α-methyl-L -valine [(αMe)Val] residue at the C-terminus, have been assessed by x-ray diffraction analysis. In all of the compounds the  (Aib)₄ sequence is folded in a regular 3₁₀-helical conformation. In the four pentapeptides characterized by the L -(αMe)Val residue two conformationally distinct molecules occur in the asymmetric unit. Conversely, only one molecule is observed in the asymmetric unit of two pentapeptides with the C-terminal L -Val residue. In the L -Val based peptides the helical screw sense of the  (Aib)₄ sequence is right-handed, whereas in the L  (αMe)Val analogues both right- and left-handed helical screw senses concomitantly occur in the two crystallographically independent molecules. © 1998 John Wiley & Sons, Inc. Biopoly 46: 433–443, 1998     

Autophagy in Spinocerebellar ataxia type 2, a dysregulated pathway,and a target for therapy

Spinocerebellar ataxia type 2 (SCA2) is an incurable and genetic neurodegenerative disorder. The disease is characterized by progressive degeneration of several brain regions, resulting in severe motor and non-motor clinical manifestations. The mutation causing SCA2 disease is an abnormal expansion of CAG trinucleotide repeats in the ATXN2 gene, leading to a toxic expanded polyglutamine segment in the translated ataxin-2 protein. While the genetic cause is well established, the exact mechanisms behind neuronal death induced by mutant ataxin-2 are not yet completely understood. Thus, the goal of this study is to investigate the role of autophagy in SCA2 pathogenesis and investigate its suitability as a target for therapeutic intervention. For that, we developed and characterized a new striatal lentiviral mouse model that resembled several neuropathological hallmarks observed in SCA2 disease, including formation of aggregates, neuronal marker loss, cell death and neuroinflammation. In this new model, we analyzed autophagic markers, which were also analyzed in a SCA2 cellular model and in human post-mortem brain samples. Our results showed altered levels of SQSTM1 and LC3B in cells and tissues expressing mutant ataxin-2. Moreover, an abnormal accumulation of these markers was detected in SCA2 patients’ striatum and cerebellum. Importantly, the molecular activation of autophagy, using the compound cordycepin, mitigated the phenotypic alterations observed in disease models. Overall, our study suggests an important role for autophagy in the context of SCA2 pathology, proposing that targeting this pathway could be a potential target to treat SCA2 patients.Subject terms: Diseases of the nervous system, Molecular neuroscience     

Latitudinal and altitudinal patterns of plant community diversity on mountain summits across the tropical Andes

The high tropical Andes host one of the richest alpine floras of the world, with exceptionally high levels of endemism and turnover rates. Yet, little is known about the patterns and processes that structure altitudinal and latitudinal variation in plant community diversity. Herein we present the first continental‐scale comparative study of plant community diversity on summits of the tropical Andes. Data were obtained from 792 permanent vegetation plots (1 m²) within 50 summits, distributed along a 4200 km transect; summit elevations ranged between 3220 and 5498 m a.s.l. We analyzed the plant community data to assess: 1) differences in species abundance patterns in summits across the region, 2) the role of geographic distance in explaining floristic similarity and 3) the importance of altitudinal and latitudinal environmental gradients in explaining plant community composition and richness. On the basis of species abundance patterns, our summit communities were separated into two major groups: Puna and Páramo. Floristic similarity declined with increasing geographic distance between study‐sites, the correlation being stronger in the more insular Páramo than in the Puna (corresponding to higher species turnover rates within the Páramo). Ordination analysis (CCA) showed that precipitation, maximum temperature and rock cover were the strongest predictors of community similarity across all summits. Generalized linear model (GLM) quasi‐Poisson regression indicated that across all summits species richness increased with maximum air temperature and above‐ground necromass and decreased on summits where scree was the dominant substrate. Our results point to different environmental variables as key factors for explaining vertical and latitudinal species turnover and species richness patterns on high Andean summits, offering a powerful tool to detect contrasting latitudinal and altitudinal effects of climate change across the tropical Andes.     

A flexible parametric model for a balanced account of forest carbon fluxes in LCA

Purpose

Despite a mature debate on the importance of a time-dependent account of carbon fluxes in life cycle assessments (LCA) of forestry products, static accounts of fluxes are still common. Time-explicit inventory of carbon fluxes is not available to LCA practitioners, since the most commonly used life cycle inventory (LCI) databases use a static approach. Existing forest models are typically applied to specific study fields for which the detailed input parameters required are available. This paper presents a simplified parametric model to obtain a time-explicit balanced account of the carbon fluxes in a forest for use in LCA. The model was applied to the case of spruce as an example.

Methods

The model calculated endogenous and exogenous carbon fluxes in tons of carbon per hectare. It was designed to allow users to choose (a) the carbon pools to be included in the analysis (aboveground and belowground carbon pools, only aboveground carbon or only carbon in stem); (b) a linear or sigmoidal dynamic function describing biomass growth; (c) a sigmoidal, negative exponential or linear dynamic function describing independently the decomposition of aboveground and belowground biomass; and (d) the forest management features such as stand type, rotation time, thinning frequency and intensity.

Results and discussion

The parametric model provides a time-dependent LCI of forest carbon fluxes per unit of product, taking into account the typically limited data available to LCA practitioners, while providing consistent and robust outcomes. The results obtained for the case study were validated with the more complex CO2FIX. The model ensures carbon balance within spatial and time delimitation defined by the user by accounting for the annual biomass degradation and production in each carbon pool. The inventory can be used in LCA studies and coupled with classic indicators (e.g. global warming potential) to accurately determine the climate impacts over time. The model is applicable globally and to any forest management practice.

Conclusions

This paper proposes a simplified and flexible forest model, which facilitates the implementation in LCA of time-dependent assessments of bio-based products.

     

Identification of a sex‐specific molecular marker in Salminus brasiliensis (Characiformes) based on SCAR marker

Salminus brasiliensis, a characin regionally named ‘dourado’ (meaning goldfish), is the biggest characid fish, this species is cited in a list of fishes that are vulnerable. The goal of the present work was to try to identify, through AFLP technique to convert them into single locus markers (SCARs), in order to improve the sex identification in S. brasiliensis. Between possible sex‐specific AFLP markers in this study, one male‐specific were isolated (Les1) and converted into a SCAR marker. Les1 marker was confirmed sex‐specific in all samples tested. A sex‐specific DNA marker applicable to fish would be very useful for elucidating sex determination mechanism in fish.     

Ontogenetic and gender-related variation in the isotopic niche within and between three species of fur seals (genus <Emphasis Type="Italic">Arctocephalus</Emphasis>)

Differences in aggressiveness when competing for environmental resources are the main factor leading to social hierarchy in group living fish. Social status acquired is related to changes in physiological parameters, as metabolic rate. Habitat variation can interfere with aggressive behaviour and promote changes in physiological parameters associated with social status. The primary goal of our study was to investigate how differences in habitat complexity affect the relationship between resting metabolic rate (RMR) and social status in the Amazonian dwarf cichlid Apistogramma agassizii. We compared agonistic interactions between pairs of males in aquaria with different habitat enrichment levels, manipulated by adding shelters. RMR was measured before and after hierarchy establishment. Habitat enrichment promotes changes in aggressive behaviour and influences differences in metabolic rate between dominant and subordinate fish. We observed an increase in biting by dominant fish at high enrichment habitat, which could be related to the increase in territory value. We observed an increase in metabolic rate in dominant fish after hierarchy establishment. However, it occurs only in enriched habitats. We concluded that habitat structure interfere with behavioural characteristics in social hierarchies, as aggressiveness, and changes in aggressive interactions affect metabolic rate in different social ranks in the dwarf cichlid Apistogramma agassizii.     

Defining the importance of landscape metrics for large branchiopod biodiversity and conservation: the case of the Iberian Peninsula and Balearic Islands

The deficiency in the distributional data of invertebrate taxa is one of the major impediments acting on the bias towards the low awareness of its conservation status. The present study sets a basic framework to understand the large branchiopods distribution in the Iberian Peninsula and Balearic Islands. Since the extensive surveys performed in the late 1980s, no more studies existed updating the information for the whole studied area. The present study fills the gap, gathering together all available information on large branchiopods distribution since 1995, and analysing the effect of human population density and several landscape characteristics on their distribution, taking into consideration different spatial scales (100 m, 1 km and 10 km). In overall, 28 large branchiopod taxa (17 anostracans, 7 notostracans and 4 spinicaudatans) are known to occur in the area. Approximately 30% of the sites hosted multiple species, with a maximum of 6 species. Significant positive co-occurring species pairs were found clustered together, forming 4 different associations of large branchiopod species. In general, species clustered in the same group showed similar responses to analysed landscape characteristics, usually showing a better fit at higher spatial scales.